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Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000007.fa

@@ -0,0 +1,52 @@
+>GCF_002008305_PROKKA_00158
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_002008305_PROKKA_01033
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKAEDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_002008305_PROKKA_01293
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_002008305_PROKKA_01383
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWR------------------KQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_002008305_PROKKA_02076
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_003691675_PROKKA_01016
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_003691675_PROKKA_01103
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_003691675_PROKKA_01111
+MRVVLLPAVADRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_003691675_PROKKA_01115
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_003691675_PROKKA_02022
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_005280335_PROKKA_01213
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_00589
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_00591
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_01251
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_01338
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_01886
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+>GCF_023573625_PROKKA_02204
+MRVVLLPAVAGRETGQIMTNSRKRHTPEQVVRKLGQADRMLADGQDVAAVCRELGVSEQT
+YYRWRNQYGGLKADDAKRLKELEKQNATLKRLLAEAELEKAALKELAEGNF
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000008.fa

@@ -0,0 +1,91 @@
+>GCF_002008305_PROKKA_00711
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_002008305_PROKKA_01398
+MEGS---------------------------------------------------LEGSH
+GDRVRLEDGRGHRGGLHHYPGLNSFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_002008305_PROKKA_01502
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------MAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_002008305_PROKKA_02225
+M-----------------------------------------------------------
+--------------------------LWK-------------------------------
+----------------------------------VRSKAP--------------------
+-----------------TVTASVSKMVVATGEGY--TTIRDSTPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_002008305_PROKKA_02227
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTVKSLEV--------
+-----------------------V
+>GCF_003691675_PROKKA_00092
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_003691675_PROKKA_00343
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_003691675_PROKKA_01013
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_003691675_PROKKA_01394
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_003691675_PROKKA_02284
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_023573625_PROKKA_00606
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_023573625_PROKKA_01016
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_023573625_PROKKA_01158
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPIADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_023573625_PROKKA_01349
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+>GCF_023573625_PROKKA_02164
+MSIHTPNTAAPALPADLEALLRQLKMPHARGIAAEVLATARAQRWEPAEVLKALLVEETT
+GRARSMLAARRKAAG---FPTGKTFTTWDPGASSIPAPTQQSLRTLEWLSRRENLVVCGP
+SGTGKTFFLEALGQQAVEEGKRVAWFTLEDLGAMIRAHRPDDTITKAVARILRADLIVID
+DIGLLPVADDAAEGLYRIVDAAYEKRSVAISSNLHPAGFDELMPKTLATATVDRLLHHAH
+VCQTTGDSVRMTQAMAGKGVMPLN
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000012.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_00156
+MK-------------------------------------GA---AQLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>GCF_002008305_PROKKA_00159
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVL--------GPAVG---
+------------------------------------------------------------
+---------
+>GCF_002008305_PROKKA_01075
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAVGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>GCF_002008305_PROKKA_02063
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>GCF_003691675_PROKKA_00297
+MRIGELAERAGTTAKTLRFYEEQGLLPPAERTPSGYRDYAPETAARIDFVHRGQAAGLTL
+AQIRQILDIRDDGAAPCEHVRDLLDARLAEIEQQIAQLAALRDTITELRRDAAQPDPDSC
+SADQVCRYL
+>GCF_003691675_PROKKA_00338
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>GCF_003691675_PROKKA_00345
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>GCF_003691675_PROKKA_00794
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGQAAGLTL
+AQIGQVLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPAMC
+SPEDVCRYL
+>GCF_005280335_PROKKA_00720
+------------------------------------------------------------
+-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+>GCF_005280335_PROKKA_00722
+MRIGEVARASGTTSKTLRYYEEVGLLPAADRTPAGYRDYGAEVLDRLDFIRRGSSPM---
+---------------------------------------------------------KWC
+SG-------
+>GCF_020097155_PROKKA_02223
+MRIGEVAAASGVTTKALRFYEERGLLPQADRATNGYRDYPEDTIVRLEFIRRSQVAGLTL
+AEILDILQIRDAGTAPCGHVRDQLAEHLTNLDRHIAELTALRETVAGLHGTAAAGDPAQC
+NAEVICSYL
+>GCF_023573625_PROKKA_01024
+------------------------------------------------------------
+-----MLDIRDRGQAPCRHVTDLLDTRLDVIDRQLAELAQLRTTIADLREDAAAGDPATC
+SPEDVCRYL
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000017.fa

@@ -0,0 +1,81 @@
+>GCF_002008305_PROKKA_00542
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS
+YLVIGKILDAAERAGADAVHPGYGFLSENADFARAVTDAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGEAVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE
+>GCF_002008305_PROKKA_01915
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRIAAGELLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAIARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLGAE-VPAGGRTSVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPADAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVAEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAISRLGA--
+>GCF_003691675_PROKKA_00267
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVTLADEAVALGGETAADS
+YLVIGKILGAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAP---ARRAT---------------------------------------------------------------
+-------------------------------------------------------------P
+>GCF_003691675_PROKKA_01611
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDKQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA--
+>GCF_005280335_PROKKA_02407
+MSIADAPQASVIPPRDPKAERRFSRVLIANRGEIAVRVVRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS
+YLLVEKILDAAERSGADAVHPGYGFLSENADFARAVEAAGLVWIGPPAEAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEHGLPVAIKAAYGGGGRGIKVARSREEIPELYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+GVVVMSTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILKEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+TEEVTGIDLVREQFRLARGEALGY-EDPVVRGHSFEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDTGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALGEAEIAGMPSVLPFHRAVVTDPAFAPEIAGAAEPFTVHTRWIETEFANHIEPS
+EHAPADPTSREPRRTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGRRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLTAHRAGVVSGLEVEPGQTVSAGTVIATIADAD
+>GCF_020097155_PROKKA_00880
+MSTPSTT-----------ASRPVTRVLIANRGEIAVRVARACRDHGIASIAVYSDPDAQAMHVAVADEAYALPGSTSAET
+YLDIAAVLDVARRSGADAVHPGYGFLSENADFAQAVIDAGLTWIGPSPQAIRDLGDKITARAIAQRAGAPLVPGSDGPVP
+DAAAARAFAQEHGLPIAIKAAFGGGGRGIKVVRELSEVEDAFESAVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+AVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRQRIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRIAAGEPLSIPEDPAPRGHAIEFRLNAEDPAHGFLPVPGPVEAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVVGEDRSQAIARARDALAELRIEGVPTVVPFHRAVLEEEAFT-----SAEALGVYTTWIESEFAAPLAAS
+PHLGAS-VPGGGRTTVTVEVDGRAVRLGLPA---DLHAALLGGGGARTGA--SAPAE--------QSVDEGAVTSPVTGT
+LASWKVEDGAQVAEGDTIAVVEAMKMETPVRAPRAGRVERAAGDAPAAVTRGQVLASVRA--
+>GCF_020097155_PROKKA_02288
+MTNASAPQASA--DIAEAPGRPFSRVLIANRGEIAVRVIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGETAADS
+YLVIQKVLDAAERSGADAVHPGYGFLSENAEFARAVEAAGLVWIGPPADAIDALGDKVSARRIATKVGAPLAPGTTSPVN
+GTDEVVAFADEFGLPVAVKAAYGGGGRGIKVARTREEIPELYESAVREAVAAFGRGECFVERFLDRPRHVETQCLADAHG
+NVVVVSTRDCSLQRRNQKLVEEAPAPFLTDEQNTRLVESSKALLKEAGYVGAGTCEFLVGQDGTLSFLEVNTRLQVEHPV
+SEEVTGIDLVREQFRIARGEALGY-GDPEARGHSFEFRLNGEDPGRNFLPAPGTLTRFRMPSGPGVRVDAGVTEGETVSG
+AFDSMVGKLIVTGADRRQALQRAARALAEAEIAGMPSVLPFHRAVVADPAFAPELAGSEEPFAVHTRWIETEFAHQIEPT
+ALTPAAAPDRPERHTVTVEVNGKRVDVTLPTWGEAMHQ--LQGAAARAGAGRRRPRGARRAGAAPAAPGTDSLTAPMQGT
+VVKVAAQNGDRVAEGDLIVVMEAMKMEQPLTAHRAGVVSGLEVAAGDALTAGAVIAVIADAE
+>GCF_023573625_PROKKA_00545
+MSIADAPQASVVPPVDPAAERRFSRVLIANRGEIAVRIIRACQDEGLTSVAVYAEPDRDALHVKLADEAVALGGESAADS
+YLVVGKILDAAERAGADAVHPGYGFLSENADFARAVADAGLVWIGPPAAAIDRLGDKVSARQLATKVGAPLAPGTTSPVT
+GTEEVVAFADEFGLPVAIKAAYGGGGRGIKVARTREEIPEFYESAVREAVAAFGRGECFVERFLDKPRHVETQCLADVHG
+DVVVISTRDCSLQRRNQKLVEEAPAPFLTDEQNARLVESSKAILQEAGYVGAGTCEFLVGQDGTISFLEVNTRLQVEHPV
+SEEITGIDLVREQFRLARGEALGY-TDPQPRGHSIEFRLNGEDPGRNFLPAPGRLTTFRMPSGPGVRVDSGVVEGETVSG
+AFDSMVAKLIVTGADRRQALQRAARALREAEIVGMPSVLPFHRAVVRDPAFAPEIAGSEEPFSVHTRWIETEFANRIEPS
+ALTPAEPAPREARHTVTVEVNGKRVDVTLPTWGEALHT--ISGAAQRAGAGRRRPRGKRGAPVA-AAVSTDALTAPMQGT
+VVKVAAENGQTVAEGDLIVVVEAMKMEQPLAAHRAGVVSGLEVEPGQTVTAGTVIATIADAE
+>GCF_023573625_PROKKA_01835
+MT--TTP-----------AARPVTRVLIANRGEIAVRVARAARDHGIASIAVYSDPDADALHVAVADEAFHLPGASSADT
+YLKIDAVLDVARRAGADAVHPGYGFLSENADFAQAVIDAGMTWIGPSPDAIRALGDKITARSLAQQAGAPLVPGSDGPVP
+DAAAARAFAEEHGLPIAIKAAFGGGGRGIRVVRELGDVEDAFEATVREAVAAFGRGECFVERFLDRPRHVEAQVLADEHG
+HVAVLGTRDCSLQRRNQKLVEEAPAPFLTDEQRERIHTSAREICRAAGYTGAGTVEYLVAPDGLISFLEVNTRLQVEHPV
+TEEVFGVDLVREQFRVAAGEPLSIPEDPTPRGHALEFRLNAEDPAYGFLPVPGPIDAFEAPTGPGVRMDSGVRTGSVVPG
+EYDSLLAKLIVWGEDRAQAVARARDALAELRIDGVPTVVPFHRAVLEQDAFT-----SGDRLGVYTTWIESEFAEPLAES
+PYLSAE-VPAGGRTAVTVELDGRAVRLGLPA---DLYAALLGGGGA--GA--AAPAGAAGAG---KPDDDGAVASPVTGT
+LASWKVEDGAEVVEGDTVAIVEAMKMETPIRAPRAGRIQLLVAETPASVTRGQAIARLGA--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000019.fa

@@ -0,0 +1,28 @@
+>GCF_003691675_PROKKA_00342
+MPAPYPQEFRDDVVRVARSREEGVTLAQIAKDFGTHEMTLSKWMRQADVEDGAKPGTTKA
+ESAENRELKKRIRLLEQENEVLRRAAAYLSQANLPGKGSTRS
+>GCF_003691675_PROKKA_01766
+MPAPYPKEFRDDVVRVAQNREPGTHLKDIAKDFGISESCLTNWIRQADIEAGNIPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>GCF_005280335_PROKKA_02275
+MPAPYPQEFRDEVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>GCF_005280335_PROKKA_02497
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>GCF_005280335_PROKKA_02616
+MPAPYPQEFRDDVVRVAQNREPGTHLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>GCF_005280335_PROKKA_02634
+MPAPYPQEFRDDVVRVAQNREPGTQLKQIAKDFGISFSCLTNWMRQAEIEAGNKPGTTKA
+EAEELRAARRRIRLLEQENEVLRRAAAYLSQANLPKK-----
+>GCF_020097155_PROKKA_01886
+MSKPYPKEFRDDVVRIARNREPGVELSQIAKDFGIHFTTLYAWMKKADIEDGDRPGTTEA
+QYAELREAKRRIRTLEQEVEVLRRAAAYLSQAHLPGK-----
+>GCF_023573625_PROKKA_00899
+MSKPYPKEFRDDVVRVARNRGPGVELSQIAKDSGIHVTTLYAWMKKADIEDGDRPGTTEA
+QSAELREAKRRIRTLEQEVEVLRRAAAYLSQAHPPGK-----
+>GCF_023573625_PROKKA_01543
+MPGPCPREFREDVVAVARSRESGVTIKQIATDFGVSEATLQNWLRQADVEDGNRPGQTAA
+DAAEARELKKRIRLLEQENEVLRRAAAYLSQANLRLGGSPK-
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000020.fa

@@ -0,0 +1,64 @@
+>GCF_002008305_PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTG-
+--KGGKKSRRAAR----------AKKG----------------------------------
+>GCF_003691675_PROKKA_00245
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGVVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHELFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLS-GVGS
+SAKKGRRSRRKAR----------TR-G----------------------------------
+>GCF_003691675_PROKKA_00256
+MNIIDFLRVLRANRLVILGCAALGLALGLLYSLLQPTLYTATSTAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS
+RTVRERIAAE-GLDTAGATL----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA
+MEDALAPAAPSSPDRVRHLLYGLGAGLVLGLIVAFLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP
+-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA
+VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAAEA-AAGT
+A---GDASRR---------------------------------------------------
+>GCF_005280335_PROKKA_01211
+MDLQQYLQTFRKYWRSILTVLSVCVGAALVFTFLQTPKYSSTSSALIAVDT--AATPGELSSGALYAERQVSSFVALADS
+ALVLDPVINELGLNVTPQALRSRVSVSAPAGTSIVDVTVTDTNAGRAAEVANAITASLKNVTSDVVPTGPDGDEIVTVTV
+VEPAAASSRPVSPRPVVNIALGLIAGVVIGLGQALVRRLLDSRIRTRDDLVEITDAPVLASVVHHKGSDRPKDEAAPARG
+-TAWASAESYRKLRTAVGFVALGGERRSSIVVTSSVQGEGKTETSTNLAKVLAETGARVLLVDADLRRPQVGARLGLDDE
+LGLSDVLTGRADLNDVLLSV--DDLSVLTAGTVPPNPSELLGSEAMAELL-ALVEAHFEYVILDAPPLLPVTDAAILSHQ
+AGGAIVVARSGVARQNQLAEALSILEAADASVYGVVLNDVPVSHIDG--------------YSQYYR-------------
+-------------------------------------------------------------
+>GCF_005280335_PROKKA_02417
+MNIIDFLRVLRANRLVILGCAALGLVAGLVYSLLQPTLYTATSTGFVTVQG--EAT----ISGTETAQTRAQSYIPLINS
+RTVREKIAEG-GLDTAGASL----SAAVVPGSNLITVSAESEDPEQAAALANSALVATAETANGLDPTSN-----VQVTA
+MEDALAPTSPTSPDYVRNMLYGLGAGLLLGLVIAVLRRILDVNVRTTTDAQVASGAGLLGAI--PLDATLKAERDAPRGE
+-PSPRAAEAVRQLRTNLRFAAVDDPPR-TIAFTSANPGEGKSTVIGSLALAVAASGQPVILIDADLRRPRQALQFGVDGR
+VGLSEVLNGDVALQDVLVPVGDHGLLLLPAGRTPPNPSEQLGSARMRDLLTALAETHM--VLVDAPPVLPVTDSTLLSTA
+VDGTVLVVRHGKARKEHVEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGSYASKGDDYHAYYQASRDAESR-PSDE
+AVPEGPAAQR---------------------------------------------------
+>GCF_020097155_PROKKA_02299
+MNILDFLRVLRANRLVLLGGVVLGLLGGLVYSLLQPTLYTSTSTGFVTVAG--EAS----ISGTETALTRAQSYVPLINS
+RTVREKVAES-GVDVSGSTL----SAQVVPNSNLITVTALAPDPQRAADLANTALGATAEVANSLDPTSN-----VKVTA
+MEDALPPAGPSSPDHLRNALIGAGIGLLAALAVAFLRRVLDVNVRTTTDATEASGAGLLGAI--PQDGTMKAERTAPLGV
+-PSPRAAEALRQLRTNLRFAAVDDPPR-VVMVTSSNPGEGKSTVIAGLAQAVAVSGQPVILVDADLRRPRQASQFGVDGR
+VGLSEVLSGDVLLEDAVQDLG-DGLLLLPAGRTPPNPSEQLGSHRMQELLRVLAETHL--VLVDAPP----------GAA
+GDG--LHPAGGRRGRDR-------------------AGGAPRQDPEGPCGGGPGHAGQGQRPHAGRGAQRRARLRCGLGL
+LRRGLRRGRRQLRRLLPGAPGRRRRRGRDRGRHVATLIAPGGRARSSHRRRRPGDAEGPRL
+>GCF_023573625_PROKKA_00524
+MTIVDFFRLLRANLLLLLAAALVGGLLGWGYSALQPRIYASESQGFLAARAADQSL----ITSNLPAESRAQAYVALINS
+EAVRERVAQD-TGQDGDGSL----SAVLVPESSMIKVTATSTDPETAAQLANSALQATADVAADVDKNSP-----LEVVP
+LSDARVPSAPVSPDTRRNVLLGAVAGLGAGLAIAVLRRLLDVKVRSRADVKEITGAGVIGAV--PENASLT--RTGEEAV
+DLDPRAGEAIRALRTNLKFVSVDEPPR-VVSFTSADPSEGKSTVASNLARALALAGERVLVVDADLRRPRQHDLFQVAGD
+VGLSEVLAGEVQPDDALAATGIPNLTLLPAGRTPPNPSELLGSKRMRALLKLASEDFF--VIVDSPPLLPVTDGSLLATA
+VDGTVLVVRQGRTRKDHLEAAVENLAAVDAHLLGVVMNGVARSQRGGGYSYGYGY-------ESTYHKSHDKYLQ-GTGT
+AGKGGKKSRRAAR----------AKKG----------------------------------
+>GCF_023573625_PROKKA_00535
+MNIIDFLRVLRANRLVILGCAALGLAMGLVYSLLQPTLYTATSSAFVTVEG--EAS----ISGTETAQTRAQSYIPLINS
+RTVRERIASE-GLDTAGATM----SAALVPNSNLITVSAVAPDAQQAAALANGALVATADVANELDPTSN-----VKVTA
+MEDALAPATPSSPDRVRHLLYGLGAGLVLGLIVALLRRLLDVNVRTTTDAQVAGGAGLLGAI--PLDPSMKAERTAPMAP
+-LSPRASEAVRQLRTNLRFAAVDDPPR-TIAFTSSNPGEGKSTVIGNLALTVAAAGQPVILIDADLRRPRQAMQFGVDGR
+VGLSEVLNGDVALQDVLIPVGEDGLLLLPAGRTPPNPSEQLGSERMRDLLTALAETHM--VLVDAPPVLPVTDSTLLATA
+VDGTVLVIRHGKTRKEHLEVARDMLAGVNARVLGVVLNGTPASGVGSDY-YGGGYGADGGSYDAYYQAPRDAPEA-AAGT
+A---GDTSRR---------------------------------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000021.fa

@@ -0,0 +1,73 @@
+>GCF_002008305_PROKKA_00570
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------MHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA
+PS-ETSAPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAVLGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP
+AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGTVLAARLPA---AP---
+>GCF_002008305_PROKKA_00571
+MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWLLWVFAGLVLASGVLDAVVDTAQNAQGLQV-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------
+>GCF_003691675_PROKKA_00294
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------MHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPVDSASARGAADQSPA
+PS-ETSTPPAPAAQALP--RRAAVAVLVPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPEPVAVP
+AAFAGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGAVLAARLPA---AP---
+>GCF_003691675_PROKKA_00295
+MSEAPPHLPTADDGVAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWPLWVFAGLVVASGVLDAVVDTAQNAQGLQV-------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------
+>GCF_005280335_PROKKA_02374
+MPSASPSSPAARRARAHPVARRDVVRARWAATLAFLTNGGMLGALIPHYPQAKAAFGLDA
+DAFGLLVVALAAGAAAAGSLPAPVLRRWGSRRVMLAGTVVMAVVVVAAGLVVDLSAPAQG
+R------PWAGAVWLFAALLGVAGILDAVVDTAQNAQGLTVQTRLARPVLTSMHAGWSLG
+AGLGAGLGALAVGAGMPAGLHLGLNGAACVAVLVAAGRRFLPD------------DARPA
+P-----DADAPEGTAAPAPGPSP-------------------------------------
+-----------------------------RRPAR----------------PPPPRP-APP
+---------------------------PGWPC----------------------------
+-----------------------------SP---
+>GCF_005280335_PROKKA_02375
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------MAGFGVEEFGNAWTALFLQSERGLDV
+AAAGLGASTLLLAQFVGRLVGDRVLHRLGRRRTLAGSLAVVVAALVLVLTAP-----AAP
+AVFAGLALAGLGCAVVVPTAYALGDEVPGLPPRTGLAVVSWLMRVAGIGLSPLVGLLATG
+LPLPAALAVFPALAVLGLVGTGVVGRRRRRP---
+>GCF_020097155_PROKKA_02254
+MTSAPADTPR--------IDRRAATRSRWAATAAFFTNGALAAAMIPHYPQAKAAFGLDP
+AGFGLLVTVMTLGAACAGPAGAPILRRAGSRATVLWGSLAIAVVLTGAGLALDLGARSDA
+AG-----PWLGA---YAAAVFASGLCDAVVDTAQNAQGLRAQHALGRPVLTSMHAGWSLG
+AAVGAALGAAAVGAGVPAGLHLGLNGAACVLLLALTLPRFLPDTP----------DHAPA
+PALLTADDPGPESEATPASHRHPWLLLAPIVVISMAGFSVEEFGNSWTSLFLQAERGLDP
+ATAGLGASTLLGAQFLGRLTGDRVLAALGRTRALTGGLAVVLAGLTVTLLVP-----TPA
+AMFTGLALAGLGSAVVVPTAFALADEVPGLPAQTGLAVVSWLMRLAGLGLSPLVGLLAGV
+LPLTAALGAFVVLAALGTVLALTLRAPRLAPDFR
+>GCF_023573625_PROKKA_00572
+MSEAPPHLPTADDGFAR------ARRARWAVTAAFATNGALLGALIPHYPEAKAAFGLDP
+AAFGLLVIALAVGGTLAGPLPAPILRRFGARRVMLAGSVAIALLTTAAGLVLDIAGAGAG
+AGHGAGTAAAWPLWVFAGLVLASGVLDAVVDTAQNAQGLQVQTRLARPVLTTMHAGWSLG
+AAAGAGLGAAVITVGGPAALHLGLNGAVCVAVLLGVRRLFLAEAPTDSASARDASDQSPA
+PS-ETSTPPAPAAQALP--RRAAVAALLPAVVIAMAGFGVEEFGNAWATLFLITERGLDP
+AAAVLGASTLLGAQFVGRLAGDRTLAALGRRGALTAGLGAVVVGLGLAL-APLPGPVAVP
+AAFVGLALAGLGCAVVVPVAYALGDEAPGLRPQTGLAVTSWCMRLAGVGLSPAVGALAGA
+VGLAPALTVFLGLAAVGAVLAARLPA---AP---
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000026.fa

@@ -0,0 +1,56 @@
+>GCF_002008305_PROKKA_00134
+MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED
+>GCF_003691675_PROKKA_02148
+MS------------------------------TSPSGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED
+>GCF_005280335_PROKKA_00251
+MS------------------------------TSPSGSRVAE---PGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLIAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+AYMAFWFPEVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQAGLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGVRKAAAVHDRTGTLPVASGEEAAASHR
+>GCF_020097155_PROKKA_00186
+MN------------------------------ASPSGAHAVDHPRDDAAHAAQSQLHRGLSQRHIMFIALGTAIGTGLFY
+GSAGGIQTAGPGVILSFLIAGFAVYLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAVT
+KYMAFWFPGVPAWAWVAATILVIGLVNLTHVGNFGEAEFWLTLIKIGAIVAMIFGGLILMFTGASFTDGTPAGLHNLVDH
+GGFLPHGFGGVLIALTIVTFSFGGIETLGVAAGEAKDPETALPKAINTVPVRILLFYVLTMVVIMSLVPWSAVDGKTSPF
+VQIFEGLGVPFAPHILNFVVLTAAISAINACIYASGRLLYAMAHDGQAPRAFTRTTANGVPWLTVAVMLGVMVLGAILIT
+VNP-DAFGLIAGVASFAVVLTWTMIFLSHRAMRARVKEAGAPPSVYPMPFGIVGTVLGLAFVATVVITMATI--------
+---PESRQA-----LLIGLAWVVALTAAWFVTGVRKTAALHDRTGQLPVVHRHH------
+>GCF_020097155_PROKKA_00187
+MQ------------------------------STPA-----------PEAPAQAQLQRGLNPRHITFIALGTAVGTGLFY
+GSAAGIQAAGPGVVLAFMLAGAAVYLVMRALGEMAVREPISGSFVAYASRYLGPFAGFLTGWTYVFELAVVIVADTTAVT
+VYMAFWYPDVPAWVWVAATMVVLGLINVTHVGSFGEAEFWFSLIKVLAIVGMIFGGVILMFSGASFQDGVTPGPHNLVEH
+GGFLPHGLMGVLTALTIVTFSFGGTETLGIAAGEAEDPASALPRAVNTVPVRILFFYIGSMLVIMSLVPWTTVDGETSPF
+VQIFETLGVPFAPHLLNFVVLTAAVSAINACIFTNARLLHHMAHDGHAPRVFTAVTRGGVPWVTVVAMLGVMAAGAVFMS
+VKE-DTFGIVAGVATFAVVFTWALILASHLGMRRALARHGQAPGAFPMPGGRVGAWLGLAFVAVVAGTMAFDQGGAVLGA
+LGGPDALQTALAQPFVIGVLWLAVLAAAWAVPAVRRSAHRHDRHGTPPPLTWDV------
+>GCF_020097155_PROKKA_02180
+MTPERRGPGTSPGGRYGVRVNEPPALPEPTGAAPPAPSPAGGATAAPSHGAADARLRRGLSMRHIQFIALGSAIGTGLFY
+GSATAIQLAGPAVILAYLVAGAAVFMVMRALGELAVRHPVPGSFGQYADRYLGPFAGFVTGWTFVFEMVVVAIADVTAFG
+VYMGFWFPDTPRWIWVTAVILFIAAVNTRHVKVFGELEFWLSIVKVSAILAMVIGGVALLVMGVSLDAATPAGVQNLVDH
+GGFAPHGAAGVLAALSVVVFAFGGVETIGITAGEAQDPGRAIPRAVNAVPARILLFYVMTMVVIMSLVPWDRITGEASPF
+VEIFSTLGVPAAPAILNLVVITAAISAINADTFSAGRMLFGMAQQGRAPAVFASVSRGGVPWMAAVVMGLALAVGAVLNA
+VIPEDVFVVVASIATFATVWVWLMILLAHIAMRREVARRGLPASAFPVPLWPAASWAAVAFVLLVVGLLGWF--------
+---SDTRVA-----MIVGLVWLVLLGAAY-----RLFLHGHGR--SRPDLEEGAA--SSP
+>GCF_023573625_PROKKA_00142
+MS------------------------------TSPFGSRVAE---TGAATADRGQLHRGLSQRHIMFIALGTAVGTGLFY
+GSAGGIQAAGPGVILSFLVAGAAVFLVMRALGEMTLREPVSGSFAAYASRYLGPFAGYVTGWTFVFELAVVIVADTAAIT
+TYMAFWFPGVPAWAWVAATILVVGLINFTHVGNFGEAEFWLTLVKVGAIVAMIFGGVILLFTGASTADGTQASLANLVDH
+GGFLPHGILGVLTALTIVTFSFGGIETLGVAAGEAKNPEKVLPKAINTVPIRILLFYVLTMAVIMALVPWNQVDGKASPF
+VQIFEGLGVPFAPHLLNFVVLTAAVSAINACIYASGRLLYAMAHDGQAPRAFTHTNRGGVPWLSVAVMLGVMVLGAVLIT
+VDP-NAFSLVAGVASFAVVLTWAMIFLSHRAMRRRVAEQGAEPSPFPMPLGGVGTYLGLAFVATVVITMATI--------
+---PDSRQA-----LIIGLVWVAVLTLAWFVTGTRTSAAAHDRTGTLPVVRTRQS--HED

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000027.fa

@@ -0,0 +1,15 @@
+>GCF_002008305_PROKKA_00161
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_002008305_PROKKA_01073
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_003691675_PROKKA_00336
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_003691675_PROKKA_00347
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_003691675_PROKKA_00792
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_005280335_PROKKA_00724
+MTAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+>GCF_023573625_PROKKA_01022
+MAAKHGKGPGPDEGQRPARRGVVLTLLGIGLVAAAYVVTIVVMVVR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000028.fa

@@ -0,0 +1,50 @@
+>GCF_002008305_PROKKA_00162
+MSTPATRGRADGGAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_002008305_PROKKA_01072
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_003691675_PROKKA_00335
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_003691675_PROKKA_00348
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_003691675_PROKKA_00791
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLHDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_005280335_PROKKA_00725
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGTKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+>GCF_023573625_PROKKA_01021
+M-----------GAGHSHAPATGHAGGRYRRRLAGAFALTAGFFLIELVAGLVSGSLALL
+SDAGHMAADVVVLGAALLATRIASRPDSTGRRTYGSYRAEVFASALAVLAMLAVGVYVVV
+EAISRLGDAPEVASGAMLAVGFAGLVINIISMLLLRSGAKDSLNVKGAYYEVIADAAGSV
+GVMVAGVLIILTGQPIWDVVVAALIAVFVIIRAVVLGRQVIAVLGQHAPEGVDPEDVAGD
+LDAVEGVEEVHDLHLWTLTSGMNVATAHLVADQGADHGAVLAGARRVLRDRYGIAHATLQ
+VEGAGSDGCHDLSW
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000029.fa

@@ -0,0 +1,29 @@
+>GCF_002008305_PROKKA_00163
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_002008305_PROKKA_01071
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_003691675_PROKKA_00334
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_003691675_PROKKA_00349
+MSVTLLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARALYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_003691675_PROKKA_00790
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_005280335_PROKKA_00726
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLADPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+>GCF_023573625_PROKKA_01020
+MSVTPLDSCQVTAVHPEKVALTRERIPDEREAGRLAGLFKLLGDPRRARVLYALLEAGEL
+CVCDLAASVDVAEASVSQVLRVLRTAGVVENRREGRMVYYRLADGHVRMLLDVSREHARH
+EGQG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000031.fa

@@ -0,0 +1,64 @@
+>GCF_002008305_PROKKA_00172
+---------------------MPGRLIGW-----PRKPTLLELLFG--------------
+---LAMWEHAVMQIISFFNHKGGVGKTTMLFNAAVEMGRLGKRILMVDFDAQANLTAISI
+DDDMLSMIYAPDEDGKTVAHAFAPLVGGSGDVFAPEAIEVREGKVWLAAGDLRLSEFDAI
+LPSAWTEALAGNERGFRVTSAPYRLICEIAEE---------IKADY--VFVDLGPNV--G
+ALNRAVLLGSDYMIIPMAADLFSIRALPSVGNSVDTWVRQWNTARSVAPRL----NFD--
+IQKGLPKVLGYVSQQFNIYRGEATLAFSHWIDEMPAQIQSGLLEPLAVHSDGKGATLADP
+AQSKGPGVGDLKNFHSLVPHAQTLRKAIFELRADDVVRGGQVTRARQSEEQFKELCANII
+ARAV
+>GCF_002008305_PROKKA_01408
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIS-------RGG--------------------
+--AP
+>GCF_003691675_PROKKA_01138
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>GCF_005280335_PROKKA_01488
+---------------------MQTSLEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLSSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA---
+-----GLGANPHDLETTVYN-----VLMERSVTA----------------------RDAI
+LPTPF-EGMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDKVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>GCF_020097155_PROKKA_01399
+--------------------------------MTPKEPIPVMTVHGEPVLGPTGRPKHEF
+PEPTPLAGHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRKVLMVDFDPQGALSA---
+-----GLGADPYELDVTVYN-----VLMERKVTA----------------------RDAI
+LPTAF-ENMDVLPANIDLSAAEVQLVNEVAREQVLDRALRQVKDDYDVVLIDCQPSL--G
+LLTVNALTASDGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVDGFGDRVFETVIKRS----IKFADA
+TVAATP-ITVFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+>GCF_020097155_PROKKA_02230
+------------------------------------------------------------
+-----------MHTLMVYSEAGGVAKTTTAVSLAMSWAEQGRQVVLIDLDPRAAATK---
+-----WVDVEPTEPGLHIGA-----VIGNPDPTG-----------WV---------QDLA
+VPSGWHENLRVVPSDRSLSHQESDRADHAHLR--LRMALSDLQADL--VVIDC-PNRQGG
+PLTQNAFTASDGVIYAARPTSDGCDGVHGARQSVA----------AFKQSMALLGAPDRL
+VE-----VGIVVSDYRD----HITPKDQTVAVEELRETGLLLTPLVPARS-----IVPKA
+RLACDW-LGRYEKGEPVAAAYADLAGLIFE-------R--------------------I-
+--TA
+>GCF_023573625_PROKKA_01358
+MGEDPDTPTTAAAARRGPRPGVQTTVEGAGAAVTSREPIPVMTIHGEPVLGPTGRPKHDF
+PEPAPLTSHGPARIISMVNQKGGVGKTTSTINLGAALAGYGRRVLMVDFDPQGALSA---
+-----GLGANPHELDTTVYN-----VLMERSVTA----------------------KDAI
+LSTDF-ENMDLLPANIDLSAAEVQLVNEVAREQVLERALRQVRDDYDVVLIDCQPSL--G
+LLTVNALTASHGVIIPLTAEFFALRAVALLVETIE----------KVQDRL----NPD--
+LE-----IDGVLATMFD----QRTLHSKEVVGSLVAGFGDRVFETVIKRS----IKFADA
+TVAATP-ITLFAENHDGAKAYRQLARELIC-------RGG--------------------
+--AP
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000032.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_00245
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI
+AFERRVFHAAFATADQKEGMDAFTAKREAGWQHR------
+>GCF_003691675_PROKKA_00096
+MST-----------GLHIETVDRIGIIRLDRPAELNALTFATVEEIAAQVQRWEVDGETD
+GVVITGSGQKAFAAGADIREL------QHKSVQEMTARGMQHAMTALRESSLISVAAVNG
+LALGGGFELALSCDIRLATPQASFGLPELGLGIIPGAGGTQLLTRYTNASVASYHILTGQ
+PISADRAHQLGLVSELHEAEDLMAAAMEVIGTIASKGPLARQLAKRAIHGAAHAGMDSGL
+EIELLAQAAIFGTQEREEGLNAFLERRTPSFIPRPRPRKD
+>GCF_003691675_PROKKA_00100
+MTD-----------RIRTSVEQGVCTITLNRPGALNALENTMIATIVAELERAGADPDVR
+AILLRGEG-KAFCAGDDLVDMGTEEHPESPDLVERYSRGYPAIVERMLTLEKPIVASVRR
+YALGAGLEMALAADLIVAEPQAKLGLPFVLRGI---AAGTSLLPKRAPVQLVQRMLYLGE
+MITAEDAHRMGVVGHLAEDEDVDELALATARRLAVGATRAIGLMKTALRTSETLSARDAL
+AVQVGATAASVLTEDFTEGKVAFTQKRDPEFGGR------
+>GCF_003691675_PROKKA_02257
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEALEVAATIASKSKPASWMAKEAVNAAFETTLAQGI
+AFERRVFHSAFATADQKEGMDAFTAKREAGWQHR------
+>GCF_005280335_PROKKA_00124
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDPEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEAQEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI
+AFERRVFHSAFATTDQKEGMDAFANKREAGWQHR------
+>GCF_020097155_PROKKA_00093
+MNEQNRTEAAEAEQPVIVGRDGRVGRIQLNRPKALNALNAATMEAVVAAAVEMDADPEVG
+AILLLGSA-KAFAAGADIKEM------KDKDAADMYAADWFRRWEDLARLRTPIVACVQG
+YALGGGCELAMMADVLVAGRSAKFGQPEITLGVLPGMGGSQRLTKSVGKAKAMDMVLTGR
+MVEAEEAERMGLVSRLVEDEDAVATAEEVAATIAGFSKPVAQMNKEVVLNAFETPLTQGL
+VFERRVFHGVFSSEDQAEGMAAFAEKRSPVWKHR------
+>GCF_023573625_PROKKA_00245
+MSEQTTPDGAES--PIIVERQGRVGHIRLNRPKALNALNEATMRAVVAAVQELDTDLEIG
+AILLSGSP-KAFAAGADIKEM------ATKEFSEMYAADWFAGWDGLTRARTPIVACVTG
+YALGGGCELAMMADVLVAGEGAKFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMILTGR
+MIGAEEAERIGLVSRVVADEKALEEAKEVAAAIASKSKPAAWMAKETVNAAFETTLAQGI
+AFERRVFHSAFATADQKEGMDAFTAKREAGWRHR------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000035.fa

@@ -0,0 +1,22 @@
+>GCF_002008305_PROKKA_00627
+MPAAYPREFRQDVVAIARKGQIPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>GCF_003691675_PROKKA_00372
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>GCF_005280335_PROKKA_00389
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>GCF_005280335_PROKKA_00393
+MPAAYHREFRQDVIAIARKGQMPIAQVAKDFGIAESRLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLVQSPK
+>GCF_005280335_PROKKA_00410
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGVTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>GCF_020097155_PROKKA_02189
+MPAAYPREFRQDVVAIARNGQMPIAQVAKDLGITASCLRRWLAQDDVEAGIRPGLTKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+>GCF_023573625_PROKKA_00604
+MPAAYPREFRQDVVAIARKGQMPIAQVAKDFGIAESCLRRWLAQDDVEAGIRPGITKAEN
+EELKALKRRNRELEMENEVLRRAAAYLSQANLKLGQSPK
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000036.fa

@@ -0,0 +1,56 @@
+>GCF_002008305_PROKKA_00631
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP--
+>GCF_005280335_PROKKA_00403
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFREHLEPA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQAHGGTLSATSTT--AGATFTIDLPTKQPPDQPTYRRTRSSTVNTGAP---PLA
+>GCF_005280335_PROKKA_01253
+M-------------RTRLSTLLALVLVLSLAVSGITAYAVLRITVNDRIEASLQRAVEQVALLSETGVDPETGEPPDSAA
+AFIRLAMLRVLPHDNEGILG---LAPDRAELAASDAVELRLEEDPELVAWALARVGDQEARAETVTTASATYRAVVVPVT
+GWGQDDAGALLLAVDVDAEVGRLDRTFLGFAGGALLTTVFALAVGVPLLRRVFAPLESLQEAVGEVTEHDLDRRVEVIGH
+-DDVAALGHSFNAMLER-----LEDSFASQRRLLDDAGHELRTPVTIVQGHLEVMDPDDPADV----RETTRLTLDELDR
+MSRLVDDLLVLAKAQHPDF-LRPAPVDV--AELTRGVL-----ARASGFDGHVWELDGV-AEATVSLDAQRITQAWLQLA
+AN---AVRYSEPGS-----------------VVRLGSAVEGDTLRLWVQDHGVGVRPEDRAQIFERFGRGAHGTRAD---
+------GSGLGLAIVSSIAAAHGGEVSLDSVPG-LGSVFRIELPLSTPSRPAG----------SLTPGKDP-A
+>GCF_005280335_PROKKA_01330
+MTRSKPTGRLSASGRARVVAWILGVSALGMVLMLVSIVLTLRWVERDAIETSLTQESDEVAVFAQNGRDPETGEPFATPE
+RFVGHYLERQRVEPTELMFGGTAATPVIAQIHGDAA------APVELLAPATRQ-AMEQPRSRGTLVDPTHGRISYANLT
+VTTPADTGHVVVAVFHERYEQRVMTQTLLLSALALAALAATAAAAWLVSSRILGHTVEFHRAVDASLKDRGLRRLPENGS
+-EEYAGLARRANDLVRR-----ADRRLEEERRFAEDVTFALRTPLTVIEGGL-----RNPGGDEQERRTSYRHIGAEATR
+VRGLLEDLVILSRLQQDDVVLERTPVDV--GVLVATAAQAWRERHPDAADEPRLDVEAPAEGLTAVTDRARLVQVLEELL
+DNARHAVRFAPGSDLPRDLTAVTPLERTLSVRVREEERDGEPWAVVEVADRGRGIPEEDREEVFERLANASNDPYP----
+------GNGLGLPVAALLSTALDGELTLEPGPGAAGTVARLAVPLTADQDGEDA-------------------
+>GCF_020097155_PROKKA_00451
+M-------------------------------------------------------------------------------
+------------SPTPALRGRPAPGP-----------------DAALVARAARRIGLRTALACAALVLGGAG--VFFGY-
+-------------------------------------------LWWQIAHPGVDPRDA--DATVTVQLDLVDLATAAILA
+GAAAVLITGFASLWFSRSAVQPLADALRRQREFVSNASHELRTPLTVLSARTQVLQARVPAGDPL--EPLADELRRDTDV
+MAGVVEDMLSTAR-------LDSAPEGMCDAGEVAAAACA--DLSLVGAEERGVRLRADLPSLPVALPEAALRRMLAALL
+DN---ALGFAPPGT-----------------EVTVSGERVRGVVELRVADRGAGIQGVEPDHVFDRFARGRPAAVPGSGP
+GAVPRSSHGIGLALVRETAHRYRGEVRVESTGP-EGTVMLLTLPAAQEAR-----------------------
+>GCF_020097155_PROKKA_02198
+MT-----------SRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGGQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLDNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSVTSTT--AGATFTIDLPTKQPPDQPTYRRTRLSTVNTGAP---PLE
+>GCF_023573625_PROKKA_00600
+MT-----------GRRRYQGLAARFFLAQLLVVGASVLAAV-------VVASL---------------------------
+-----------------------AGPPLFHEHLEQA--------------------------------------------
+GAGHDAAQML------HVEQAYRDANFWTLGVALATALICCLALTWHVARRIQSPINALTQAAKAMAGGRYDTRVPAMGA
+GTEVEELAGSFNTMAAR-----LQRTEDTRRRMLSDLAHELRTPVSVLTVYHEALQDGVSHWD----EPTGELMGEQLAR
+LTRLVEDINDVSRAEEGRIELDRSPQGV--SGLLHAATEA--HKEAYATKGVALTMDAD-PGLAVDVDRQRMGQVLGNLL
+TN---ALRHTPAGG-----------------RVTLEARQSPSGVTLSVTDTGEGISPEHLPHVFERFYRGDTARDRDHG-
+------GSGVGLAISRALIQTHGGTLSATSTT--AGATFTIDLPTKQPPTSPP----------TGAPVYPP--

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000047.fa

@@ -0,0 +1,98 @@
+>GCF_002008305_PROKKA_01806
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVER----RLE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPIVAATETADDAAAGAAPQSTPTAPETPAGPA----------------------------------------
+--------------------------------------------------------------------DARS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>GCF_003691675_PROKKA_01503
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+DGGPGPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFERQSETT---YGQPLDYTAVMDVREGTGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLVISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL
+RSAMERWWPVAAPESEEEAVASAAAVGHTGTTPETLAGPR----------------------------------------
+--------------------------------------------------------------------TPRS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>GCF_005280335_PROKKA_00397
+M------SRTEDQDPG-----RRPEVAL----PALGFWGTLRFAWTQLTSMRTALMLLLLLAVAAVPGSLFPQRPAGPGI
+VQDYIDDNPVLGEWLDR--FQMFDVYSSVWFSAIYLLLFISLIGCVAPRAVKHAQALRSAPPRTPRRLSRLPEYGRVVLE
+PGGPAPVE-------AVEQAARYLKRRGYRIEV----RQEDAGGASVGAARGYLREVGNIVFHLSLIGVLVFMATGSLLS
+YRGQKILVEGEGFANTLVAYDAFTPGSAFSEEMLTPFSMTLKRVEYVYDRQSPTH---YGQPLD----------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>GCF_005280335_PROKKA_01068
+MGDAPVSSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-ASGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YYGQKIIVEGEGFANNLVSYDSFTPGTYFSADDLQPFSLTLDSFDVVFDRESEAL---YGQPLDYTAVMQVQEGGGGEPR
+EEILKVNHPLSMDGVRVYLVGNGYAPVLTVRDGEGDIAFQGPVVTRVQDV-NFNSLVTLKVPD------ARPDQLGFVGQ
+FMPAAVEDESGVAVSVDPELYNPQLILDSYYGDLGLDGGVPQNVYVLDTETLTELNSRKNENGGIVLSQGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDEAGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPVAAATAPE-------------TTPETPCRPRRRPIRRLTVFNPTAPVNEQLALYSDLFMLIAAFVYAAAFV
+LFTIDMATSSATIRRLEEDLAAQRGPARLAPARETVGAGFGGSSLGGSSSVGSTGAGSSAGGPGVLPGEARAAGLGDEPG
+LVDEDMDYTGGGRRPIANVAVAVLAVGWALHAFAVIARGLAASRVPWGNLYEFMTTGALVITTVYLLFLFRKDLRFVGTF
+VTGLVVAMMCAATMGFPTPVGHLQPPLQSPWLVIHVSIAVLATALFTLTAAMSMLQLIQDRAEKRAAATGERPWAFLRLV
+PSAQALENWSYRINAVGFVMWTFTLIAGAIWAEASWGRYWNWDTKEVWTFVIWVVYAAYLHARATRGWTGARAAWLSIVG
+FLCVVFNYTIVNTYFPGLHSYAGLPG
+>GCF_005280335_PROKKA_02641
+M------SRPSDYDDG-----TGAGGTLRAESPELGFAGWLRWFWRQLTSMRVALILLLLLAVAAIPGSLVPQRGADPNG
+VVQYQKDHPDLFPILDAFPIQAFDVYGSVWFSAIYLLLFISLIGCVLPRIAHHWKAWRGRPPKTPARLQRMAGFSEIRLS
+NPDATPAEREAFAARAVDEAAAILKKLRYRVEVQRASRRG-VDEVSVSAERGYLRETGNLLFHVSLLGVLVSVGLGGVFT
+FNGQKVLIEGETMVNQLIDYDTATSGRSFDSSSLEPFSLRLDTLDVTYNTPDDGNVQAIGLVKDYTANMTLISPEGDE-S
+EHVIRVNHPLRVHGSPIYLIANGYAPKITIRNAEGTVVYSEAMPFIPQDNLNMTSLGVVKVPDGIVDESGEPVQLGLRGF
+FYPTKADLDTGAYTSNYPDLENPVLTLDVFVGDLGINDGIPKSVYALDTSDMEQVTGRAVDLDSIELRPGEQTELPNGFG
+TIEFESVPRYASFDVMQNPAQEWILVFAVLALGGLMWSLFVPRRRMWVKALPSEDG-VVLQYAALARGDDPALERAVEEL
+RDRHRELL------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>GCF_020097155_PROKKA_01003
+MGDAPVSSTSAPKDPAPRNRTRDD-VTL----PALGVGGTLRWAWTQLTSMRTALLLLLLLAVAAVPGSLVPQRRAGPEA
+VDQWIEDNPFWGPILDA--LQFFDVYTSVWFSAIYLLLFISLVGCVLPRALKHAKALRQPPARTPRNLGRLPESGVVVLE
+AGGPAPEE-------AVRQAQRWLKRKRYRVEL----RPE-AGGASVGAERGYLREIGNILFHFSLIGVLAFMAYGGMTK
+YTGQKIIVEGEGFANNLVAYDSFTPGMYFDAASLQPFQLTLKSFDATFERQSQTH---WGAPLDYTAVMEVRHGTGGDPE
+EQVLKVNHPLEIDGAKVYLVGNGYAPVVTVRDGNGDIAFQGPVVTRVTDQ-NFNSLAVIKAPD------ARPDQLGFVGQ
+FMPAAADVGQGVEVSVDPEPLNPKLILNSYSGDLGLDAGVPQNVYVLDTSTLTELNSRRSENGGITLSVGQTHVLPDGKG
+SISLDGVRRYVGLDIHYDAGKWGVGVFSVLALIGLAVSLFTRRRRVWVRARTGDDGRTRVEYALLARGEEFGLREEHVAL
+REAFEKMWPVSAPEADTGE-----------TTPATPA-PAAAP-------------------------------------
+--------------------------------------------------------------------TPRS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------
+>GCF_023573625_PROKKA_01727
+M-----SSKAA--------RTRSEPVTL----PRLGLAGTLRWIWTQLTSMSTALMLLLLLAVAAVPGSLVPQRRAGPEI
+VDQWIEDNPVWGPVLDA--LQFFDVYNSVWFSAIYLLLFVSLVGCVWPRAIQHAKALRQPPARTPRNLTRLPASGVVVLE
+EGGPSPEE-------AVARAQAWLRKRRYRVEH----RPE-AGGASVGAERGYLREIGNILFHVSLIGVLVFMAYGGMTK
+YGGQKIIVEGEGFANNLVAYDSFTPGTYFSADDLQPFSLTLDSFDAVFDRESETH---YGQPLDYTAVMDVREGSGGELQ
+RQILKVNQPLDIDGVRVYLVGNGYAPVVTIRDGAGDVAFQGPVVTRVFDQ-NYGSQATIKVPD------ARPDQLGFVGF
+FLPSAVEDEEGAAFSADPELLNPELQLNSYYGDLGLDTGRPQNVYVLDTASLTELNSRTNENGGIVLSPGQTYELPEGKG
+SISFDGVRRYVGLDIHYDPGKWGVGVFAGTALLGLAISLFVRRRRVWVRARTDDDGRTRVEYALLARGEEFGLHEEHVAL
+RAAMEKWWPIVAATETADDAAAGAAPQSTSTTPETPAGPA----------------------------------------
+--------------------------------------------------------------------DARS---GD---
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000048.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_01808
+MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>GCF_003691675_PROKKA_01505
+MQ--------------T-PRPSRRTVLTGLSL-LGLAPVLAACS-GDDSLTRQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--EVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>GCF_005280335_PROKKA_00398
+MPIPQPHREGHHRPPGLPPRPGRRQVLAGLAG-VASLPLLAACS-AEDPLAAQAGKADGK
+NYIAGDGSVLEIGPAERGEPVQFSSAMFSGEPIIAQDLAGDPAVLNFWYAACAPCRVEAP
+DLQALHEQFAPEGVRFLGINVRDTIATAQAFERKFGITYPSVEDRGG--QVLLAMTDYVP
+PQAVPTTIVLDHQGRVSARILGIAE-RSTLRTLITTVLDEQA------------------
+--
+>GCF_005280335_PROKKA_01066
+MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDTRG--DVLLNMADYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+>GCF_005280335_PROKKA_02643
+MN--------------------RRRTGAALALPIAALFALAGCSGGDGNLAAEWNEASGK
+GYVSGDGSSLSIAPDQRTEPVEFSGETEDGDIYGSDDTVGSVTVVNFWYAGCAPCRAEAP
+DLVEAYDEFSPQGVKFVGVNTRDQVAQARQFSVRFDIEYPSIMDNAGGRAVQRAFAGQVP
+LNAVPTTLVLDAEGRVAHRVLGQLAGASQLRTLIGETLAEAGGGAAADPASDPAPADEAT
+EQ
+>GCF_020097155_PROKKA_01001
+MP--------------FPPRPSRRAALAGLSA-AALAPLLAACSGTDDSLAQQAGNAGGK
+NYIAGDGSVVEYAADQRGAPVEFSAAGFDGETVSGETLRGEPALLNFWYAACAPCRVEAP
+HLVKLHGEFEPKGVRFLGVNVRDTVTTAQAFERTFGIPYSSVDDTSG--SVLLAMSDYVP
+PQAVPSTLVLDRQGRVAARVLGAVE-EGTLRALLDTVVAEA-------------------
+--
+>GCF_023573625_PROKKA_01729
+MH--------------TPPRPSRRTLLTGLAL-ASLAPALAACSGGDDSLARQAGNADGK
+NYIAGDGSVLEIAPAERGAPVEFAAELFDGTPVTGASLRGTPALLNFWYAACAPCRVEAP
+HLVSLHEQFAPQGVRFLGVNVRDTVTTAQAFERTFEIPYPSIEDARG--DVLLNMTDYVP
+PQAVPSTLVLDVEGRVAARVLGAVE-ESTLRALLTTVVDEAAA-----------------
+--
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000049.fa

@@ -0,0 +1,63 @@
+>GCF_002008305_PROKKA_02005
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAEENALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLSRMYVDLGEVPADDDHKVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGLAPVELVPTYAEERK
+EIAKNLIDFDKEWSTLMATPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSIFRPTTGSLGLHDLNNIFATCRPQHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>GCF_003691675_PROKKA_01715
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHKVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYQPSLLTTDATGQALAQGYPIGKRFKSGLVERS
+CDTNVKHLGHLHRADGRWRVYVFADTASPRAEDSKVAAWAKAIVEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSIFRPTTGPLGLHDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>GCF_005280335_PROKKA_00837
+MLFHHHGYVSTDPRVQPAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRSHRLEIGQADGIQAR
+SVETFQAFGFASQIIDEAYDLTSMAFWNPSSEDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAAYMKNSPTRAEP
+DYGWSFESLEDSA-EGEYPVLVTLRRTVDAQGEPLADPESGETRQVRAKYVVGADGAGSRVRKAIGHSLAGGASNHAWGV
+MDALAVSDFPDIRTKCAIHS-STGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEIIRRAQQIIRPYTLEVKDV
+AWHSVYEVGHRLTSGFDNRERVDHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGVAPAELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVADFYTKTAEFPAGFMTEYKPSILTTDATGQSLAAGFPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRSADSKVAAWAKAVEEDPRSFRNRHTPADGPQDARFDVKVVYQQKQTEFAH
+PDVPAVFRPTSGDLRLLDLNNIFATCQPKHGEDIFEARGISRDGAVVVVRPDHYVSGVFGLDEVERLNEFFAGVLLDAS-
+>GCF_020097155_PROKKA_00774
+MLFHHHGYVSTDPRMKPAAGIGLDRPAELPDEMDVLIVGTGPAGMIAAAQLAMFPDVHTRIIERRGKRLEIGQADGIQAR
+SVETFQAFGFASQIIDEAYDLTSMAFWNPSPEDEDAIVRTSLAEDDPHGVSEFPHLIVNQARILDWFAEFMKNSPTRATP
+DYGWEFVSLDDSDQDAERPVQVTLRRTVDAKGNPLAEGVAGEERVVRAKYVIGADGAGSRVRKAIGHSLSGDAANHAWGV
+MDVLADSNFPDIRTKCAIHS-SSGSILHIPREGGHLFRMYVDLGEVPADDNHKVRQTPIEEVIRRAQQIIRPYTLDVKDV
+AWSSVYEVGHRLTSGFDNRERCTHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLSGIAPAELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSMLTTDAAGQELATGFPIGKRFKSAKVERS
+CDTNVKHLGHLHTADGRWRVYVFADAAAPHDADSKVAAWAEAVEEDPQSFRNRHTPAGAPQDERFDLKVVYQQKQTEFAF
+PDVPAVFRPTTGPLGLHDLNNIFAVCRPEHAEDIFELRGVSRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-
+>GCF_023573625_PROKKA_00173
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------------------------FIAGDACHTHSAKAGQGMNVSMQDGWNLAWKLGQVLEGRSDASLLATYSEERQ
+QIAENLIEFDKAWEGMMSKRPDELEDPQAVGRFYKDNAEFPNGFATQYPASSVTGEDTHQALAAGVPIGKRFESAAVRRV
+ADTSPRQLGHLFEADGRWRLYAFAD-----EDRTAVGELADWLADSPDSPVRRFTPESADLNSVFDAKVVYQQPYQEVEL
+ADVPALFLPKMGPYQLTDKEVVFAA---DLADDIFEARGIDRGGALIIQRPDMYVAHVLPLSAREEITAFFEQNMVSASV
+>GCF_023573625_PROKKA_00174
+MR---------------------------------------------------------------------GAAD-----
+----------------------------P---------RRSLSTLPTTAVSEFPFLIVNQARVIDYFAEYAERGP-----
+---------------------------------------QGQERTVRAKYVVGCDGSRSRVRDCTGIEVVRDPSAHAWSV
+MDVLLETDFPDNRQKCGIQSDKDGTILLIPREGGFLARFYVSLGSI--DDAPRPRS------------------------
+--------------------------------------------------------------------------------
+---------------------------------------------------------------GG---GIRACSSPATPA
+TPTPPR-------------------------------------------------PARA---------------------
+--------------------------------------------------------------------------------
+>GCF_023573625_PROKKA_01943
+MLFHHHGYVSTNPRVQVAAGIGLDRPAELPDEMDVLIVGSGPAGMIAAAQLAMFPDVHTRIIERRPHRLEIGQADGIQAR
+SVETFQAFGFASEIIDEAFDLTSMAFWNPAEDDADTIVRTSLAEDDPEGVSEFPHLIVNQARILDWFAEYMKNSPTRARP
+DYGWAFETLEDTN-DGEHPVLVTLRRTVDAQGNALEDPASGPTRQVRAKYVVGADGAGSRVRKAIGHTLTGDAANHAWGV
+MDALADTDFPDIRTKCAIHS-SSGSILLIPREGGHLFRMYVDLGEVPADDNHQVRQTPLEEIIRRAQQILRPYTLDVKEV
+AWHSVYEVGHRLTSGFDNRERVAHPNVFLLGDACHTHSAKAGQGMNVSMQDGWNLGWKLGQVLSGMAPVELVPTYSEERK
+EIAKNLIDFDKEWSTLMAKPTSELGDPNEVAEFYTKTAEFPAGFMTEYRPSLLTTDATGQALAQGYPIGKRFKSALVERS
+CDTNVKHLGHLHRADGRWRVYVFADAASPRAEDSKVAAWAKAIEEDPRSFRNRHTPSDGPEDARFDIKVVYQQKQTEFAH
+PDVPSVFRPTTGSLGLHDLNNIFATCRPTHGEDIFEARGISRDGAVVVVRPDQYVSGVFGLDEVDRLNAFFAGVLLDAN-

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000052.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_02160
+MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>GCF_003691675_PROKKA_01873
+MS-SE-ETVPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREHEVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>GCF_005280335_PROKKA_00589
+MT--------TRVLLVDDQPLIRLGFAAILQSQ---DDIEVVGEAGDGAECLERAAALDP
+DVICMDVQMPRMDGIEATRALAEAG-TRAAVLILTTFDRDDFLFETLEAGASGFLLKSAE
+AEHLIDAVRVLGRGDALLDPQVTRRVLRRMASAAPEGVDGPAGVGQPRDDDGAAPGQAEA
+SDAVGKAGLTGREAEILTLMARGLSNGEIAGQLFVGESTVKTHVSNVLMKLGARDRVHAV
+IWAFEHGVAG------------
+>GCF_005280335_PROKKA_00598
+MS-TDAENAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRTLLQRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLMAHMA---------------PRLRSDHARTAECE
+HEQAAVESLTPREREVLVLMAQGSANLEIAGELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+>GCF_005280335_PROKKA_02580
+M--------------VLPDAGVRGGVRVRTSRTGVVGDIRLVEGAVSG------------
+DLDSADLLLGGVNSLGETRQVARQGRDVPPFLLVAEATIVEELSGIDASGAAAVLAYPLD
+TVELAS----VAHGIAGSGPFLSPRL--------------------PQLSVEPLG-----
+------EGLSAREAEVVVALGEGLSDAEIAQALCVSVKTVHTHVLNLRRKLGARNRAHAV
+SLARSVGPLGDACSEPGLVAAL
+>GCF_020097155_PROKKA_00520
+MSPDDAQPTPIRVALVDDQALIRSGLAMLIDSQ---PDLTVVAQASDGREAAASVAVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEHVMDAIEAGASGFLLKDAP
+PEELLAAIRTVHGGDAVIAPSTTRRLLAHMA---------------PRLRQDAARSAECA
+DEQAAVGSLTPREREVLVLMGQGAANPEIAAQLVLSEATVKTHVGRVLAKLSARDRVQAV
+LIAHRTGLVG-----------F
+>GCF_023573625_PROKKA_02104
+MS-SE-ETAPVRVALVDDQALIRSGLAMLVDSQ---PDLTVVAEAGSGREAVASVSVAGA
+DVVLMDVRMPEMDGIEATRALLRRP-DAPRVVVLTTFDLDEYAFDAIEAGASGFLLKDAP
+PEELLAAIRTVHRGDAVIAPSTTRRLLTHMA---------------PRLRSDQVRSAECE
+EQQAAVASLTPREREVLVLMAQGAANLEIAAELVLSEATVKTHVGRVLAKLGARDRVQAV
+LIAHRAGLVQ-----------F
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000053.fa

@@ -0,0 +1,36 @@
+>GCF_002008305_PROKKA_02246
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LEYFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>GCF_002008305_PROKKA_02261
+MD------HKQ--ILHDGLRRQRAALLQKLEGLSERDARLPRTPTGTNLLGLVKHAAVVE
+LEYFGETFDRPAEVQLPWAAAGQSEEDNVDMFAAEGESLEDVLEFARRCFAHADATITAL
+--------GADAHGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR
+APGNNLPVWGADRWAAHVDRLTAIAEGSGGPGRN
+>GCF_003691675_PROKKA_01948
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LECFGEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VLDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>GCF_020097155_PROKKA_00418
+MD------HKQ--ILHDGLRRQRAALLHKLEGLSERDARLPRTPTGTNLLGLVKHAAVIE
+LEYFGGTFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFVHADATITAL
+--------GADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQVGLR
+SPGNNLPPWDADRWAAHVDRLTAIAEGSGGVGWN
+>GCF_020097155_PROKKA_00422
+MGFLTPQAHGELAVLTTYALQQLAQMRTTVHGLTDEQAHSVPSASALNLTGLLLHTGEVA
+VYWTAAAASAPGEPVLPED---VNEDHSLDELVADGRPLAQVLERFDRCVEVARQNLAAV
+ADLSAPVPVPDA----PWFPADLKTWEARWALLHVTAEVARHVGHADLIRESIDGTGSY-
+-------------------ELNDLADAAAQ---G
+>GCF_023573625_PROKKA_02178
+MD------HKE--ILHQGLRRQRDALFAKLDGLPEREVRLPRTPTGTNLLGLLKHAATCE
+LEYFDEVFGRPAGIPLPWDAPGVGEEDGADLFAAEDETLEDVLDYARRCFAHADATIEAL
+--------VFDARGRVPWWPAHLAEVTLAQILSHVALDAARHAGHADILREGIDGQAGLR
+GPGDNLPGWDAERWAAHVRRLEGIARGAGPV--R
+>GCF_023573625_PROKKA_02192
+MD------HKQ--ILHDGLRRQRAALLQKLEGLSERNARLPRTPTGTNLLGLVKHAAVVE
+LEYFGETFGRPAEVQLPWAAAGQPEEDNVDMFAAEGESLEDVLEFARRCFAHADATIAAL
+--------DADAPGRVAWWPDDKAEVTLAQIIAHVALDEARHAGHADILREQIDGQAGLR
+APGNNLPPWDADRWAAHVDRLTAIAEGSGGPGRN
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000055.fa

@@ -0,0 +1,70 @@
+>GCF_003691675_PROKKA_01696
+--------------------------------------------------------------------------------
+------------------------------MEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGMRTGHRARTL
+SGGEKQRVAVARALINEPPLVLADEPTGALDQARTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGELAPQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------D
+>GCF_005280335_PROKKA_00855
+MT-------LLEVHDVDKTFHSG-GEAVPVLRGASLLVPAGEMHAVTGPSGSGKSTLLRILACLDSPDSGRVLLGGEP--
+----LPEPWSRGGDRYRNQRCGIVLQDFALMEHATALENVMLPLRYGPDRVPRGEQRRRAGEALERVGLGTRTGHRARTL
+SGGEKQRVAVARALINEPPLVLADEPTGALDQERTRDVVD-LLRGAVGPERAVVVVTHDPRVAAACDRRWHLVDGGLAPQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------D
+>GCF_005280335_PROKKA_01010
+MSDGS-APPLLELAGVLKSFK---GADRPALDGVDLTVRDGDFVAIVGPSGSGKSTLLNVLGLLDRPDGGSYRVSGTD--
+----TMSMGERERDRLRSRWFGFVFQSSHALGDEPVAVNAALGLRVQRTPPEQRDAR--AGEALALLGLSHRLDTRAKLL
+SGGERQRLAIARAIATRPRVILADEPTGNLDSVNSRIVID-HLRALHAQGATVLLITHDPEIARQADRQVRIEDGRITEL
+AGHRTAASASADMAGTGHGWSAPGAARRHRSPRSSAMLDDLVEAVSSLSTRFLRTVLLMAAFAVGIGGLVASVGLTQTAT
+DQVGALLTAAALDEVVVTVPQAEGLLDPGDGRLASWADGLAALPHVTAAGHVAQVAPADVVITRHDPSDPEPAVAISLVA
+ASSSYAGLAGLTLPSETSRTLLDSPDARLAWATPAAARALELPVTDTGMLSPGYRVWIQGHAVDVAGIVTLSERTPELDA
+SLVVTPAVMTGVAQAHPQLVVRTEAGFPYPVSQAAPLVIAPENPGSVTVRTVADLRNLRAGVSDDLGAFVGVLSGVLLVL
+AVISASTAMYLSVQARTAEIALRRAIGSPRGLIARLFLLEGALIGLAGGAVGAAVGSGVILAVSQARGWAAVLPPGAVPL
+ALGLGLVAGVVSALYPGWVASRQRPADALRG
+>GCF_020097155_PROKKA_00792
+MS-------LLEVHDVDKSFTTA-ASEVPVLRGVSLSVPAGQMHAVTGPSGSGKSTLLRILACLDSPDAGEVLLEGVP--
+----LPPPWSRGGDRHRNRRCGIVLQDFALMEHATALDNVLLPLRYGPGGGSRAEQRRRAALALDRVGLADRAHHRARTL
+SGGEKQRVAVARALINDPPLVLADEPTGALDQARTRDVVK-LLRSAVGPQRAVVVVTHDPEVAAACDQRWHLEDGRLHSQ
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------G
+>GCF_020097155_PROKKA_00870
+MTA---SAPVLTLDRVQVGYRHPDGGTRVLIESLDLTLAPGEVVGLWGRSGTGKSSLIRHLAGLSRPLAGRIAYRSPDGS
+LNGEVADLSAGDLARYRREHLGYVDQSCELIGELSALDNAAVWIHGGRIAGSACDAQETVQGLLERLGLGHRLGAPASRL
+SGGEAQRVALVRALSKRPHLIVADEPTGHLDGVTAREAIA-LLREHAEAGAAVLVASHDPLVHAAVDRAVRVGED-----
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------
+>GCF_020097155_PROKKA_00943
+MNTAPLTPPVLAARGLTKAY-----GSTHALTGVDLEIRPGESVAVMGPSGSGKTTLLHVLSGIIAPDGGRVTLAGADGT
+VH-EVTALTEEQRARLRRERLGFVFQEGLLLPELTAVENVAMPLMLN--GVDRRAAEQTAARWLGSLGLAGMEDRRPGEL
+SGGQRQRVAIARAQAVEPDVVFADEPTGALDSDTSEAVLDSLIASTVARGRTLVVVTHDPSVAAACSRLIRVRDGRIESD
+QAQAAAGTTREQV-------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+------------------------------R
+>GCF_023573625_PROKKA_00735
+MS-------LLTVHDVHRSYRGP-AGDVPVLRGVSLQVPGGGVHAIMGPSGSGKSTLLRLLACLDTPDAGSIRVAGRS--
+----LPAPWSSDGDAYRNRTCGIVLQDHLLIDRATAVDNAALPLLYARPRTSKRERRTMAAELLTRLGLGDRLHHPVGRL
+SGGERQRVAIARAVIMGPSLLLADEPTGALDEERTDEVMG-LFRSMSQPERAIVVVTHDPAVAARCDHTWRLRAGRLE--
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-------------------------------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000056.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_00025
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESIALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRGGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGATAPAPDRLVEDPPAAAPRE---PSPAPR
+VGPRPAPRRA------AAPAAPAAPSHADQPTVVMGRPVT-EPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+>GCF_003691675_PROKKA_02043
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESLALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRE---PSPAPR
+VGPRPAPRRAAAPAAPAAPAAPAAPAHADQPTVVMGRPVT-GPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+>GCF_005280335_PROKKA_00370
+MERGPVVGLLDNLERGLERAVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFDRARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDTDVRAGD
+LRVVTGLDDGSLPAPAPHDDGASPATAHGPGATATAPDRLVEDL----------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------LGGRT-P
+>GCF_005280335_PROKKA_00371
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------MGRPVT-EPSGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFSG-TGGR--A
+>GCF_020097155_PROKKA_00353
+------MGLLDNLERGLEKAVRSAFSAGGARAVQPVEIASALRHAMDDESFALSEGHTVA
+PNDFTVHFAPADFDRARTWGSTLAGELCDEVIRHAQSQGYTLPGSVRVAFHEDAQVHAGQ
+VEVDARIDDGSSPVPSPPAATSAPA----PAAARTADDR--GPRPSRAPRHGATAAPAPR
+RDPSPAPRPAPTPA--RSESARRAPAD-EQATVVMPRRTSPAPAVPWLEADGVRHPLTHE
+DMVLGRSSERADVVVPDSSVSRQHARLVRVGRSVTLIDLGSRNGVTVNGRRVDGSTVLRE
+GDRITVGQTDLVFHIDPADGRPRA
+>GCF_023573625_PROKKA_00025
+MERGPVVGLLDNLERGLERVVRSAFSAGGPRAVKPVEIASALRQAMDDESFALSEGHTVA
+PNSYVVHFSPADFERARSWGSTLASELCDEVIRHADSQGYALPGTVRVAFHPDADVRAGD
+LRVVTRLDDGSLTAPAPHDDGASPATAHGPGASAAAPDRLVEDLPAAAPRK---PSPAPR
+VGPRPAPRRA------AAPTAPAAPAHADQPTVVMGRPVA-EPAGPALELDGRMLPLDGD
+DLILGRSAERADLVIPDSSVSREHLRLLTVGSTVTLLDLGSRNGVLVNGRRVDGSVTLRD
+GDVVTVGQTELLFFGG-TGGR--A
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000058.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_00049
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE
+DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--A
+>GCF_003691675_PROKKA_02062
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GE
+DATVWPMFNGTGANVVGLQAMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPEEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFVSAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRTRFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--A
+>GCF_005280335_PROKKA_00354
+MQQIHD-PASRGFASDNYSGVHPEVLAAIAEANGGHQTAYGEDAYTGRLAEVVRGHF-GE
+DAQVWPMFNGTGANVVALQSMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLTVPTPDG
+KLTPELIDVQAWGWGDEHRAQPLVVAITQSTELGTLYTPEEIRAITEHAHARGMTVFLDG
+ARLANAAAALDLPLRAFTTDVGVDVLSLGGTKNGALGAEAVVALNPAATT----------
+--------------GMTYLRKSQMQLASKMRFVSAQLLALFDGDLYLRTARHANAMAQRL
+QDAVAAGIADGSLPGVALTQRAQVNAVFATLPAGVADRLRRSFRFYDWDEANGEVRWVCS
+FDTAEEDVDAFVAALRAELAPA--D
+>GCF_005280335_PROKKA_01608
+MSAGAPAAGLRAFASDNYAGVHPDVWAALADVDAHHAPAYGADPHTERLQEAVREAFDAP
+DAVALPVFNGTGANVVALQSMLPPWGAVVAADTSHIHHDEGGAPERMGRTKLFTVPTPDG
+RLTPELVDREAHGWGFVHRAQPAVVEIAQVTELGTVYTPEQVRALADHAHGHGMGLYMDG
+ARLFNAAAALELPLSAFTTHAGVHVVSLGGTKAGALGAEAVVVLRPEAVTLASLVPERDL
+PAD--AGPRERARLAVEYVRKSSMQLASKMRYVSAQLTALLKGDLGIRLAGHANAMAREL
+AGRV-AGI-----DGVEVTRTPEANAVFAVLDPQAADRARVRHPFYDWDAARHEVRWMTS
+WDTTAADVDSFAAALGEALSPGRRR
+>GCF_020097155_PROKKA_01503
+MSAARP-AGLRAFASDNYAGVHPDVWAAMADADADHAVSYGEDPTSAALQEKVREVF-GE
+RAFAVPVFTGTAANVLALQALTPPWGSVVTAASSHLIHDEGGAPERLGRTPLVPVPTPDG
+RLTGELAAAHVRRDGFVHASQPAVVEIAQATELGTVYSAAQVREVADAAHAAGAALYMDG
+ARLSNAAAALDLPLRAFTTDAGVDVVSYGGTKNGGLGAEAVIVLNPEAVVAARMVGPADV
+PGGDAADARDRARAALGYLRKQDMQLASKHRYLAAQLLALLTDDLGIALAAQANRMARVL
+ADAV-AGL-----DDVELARAPEANAVFARLDPDVAAEVRLRHPFYDWDAAAHEVRWMTS
+WDTTDADVESFVDALAAALRARRPR
+>GCF_023573625_PROKKA_00044
+MQRIHD-PQERGFASDNYSGVHPEVLAAIAEANGGHQVAYGEDVYTARLQEVVAQHF-GK
+DATAWPMFNGTGANVVGLQTMLPRWGAVICADTAHIHVDEGGAPEKSAGIKLLPVATDDG
+KLTPELIAAEAWGWGDEHRAQPLVVYLTQSTELGTVYTPDEVKAITDYAHEHGMRVYMDG
+ARIANAAASLGLPLRAFTTDVGVDVLSLGGTKNGALLAEAVVVLDPDAAD----------
+--------------GLVYLRKNQMQLASKMRFISAQLLALFDGDLYLRSARHANAMAARL
+RAGIEAGVADGSLAGVEFTQATDANAVFAVLPEGVADRLRARFRFYDWDAARREVRWVCG
+FDTTEEDVDAFTAALRAELVPA--V
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000061.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_00068
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAEGEESPTDEPQGRAVDTEEA
+QPATEEGEATDEPQGR
+>GCF_003691675_PROKKA_02081
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFNAEGEESPTDEPQGRAVDTEEA
+QPATEEGEATDEPQGR
+>GCF_005280335_PROKKA_00326
+MPHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDAMV
+LLPGFDLVPGCVVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHITELEHIEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWQGRADAEAELEASIARFDAAGEHSPTDEPQGRDVETEDP
+SPATEEGEEKDVPQGR
+>GCF_020097155_PROKKA_00266
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+FLPGFDLVPGCIVEARPVGVFNMTDDGGGDAKLLCVPA-DKRFDHIQELEDVEESLKQEI
+EHFFTRYKDLEPGKWVKADGWEGREAAEKELEASIERFAAEGEHSPSDEPQGRDVDTEEA
+APAAEQEA--------
+>GCF_020097155_PROKKA_00684
+MLFDVTIEIPRGSGNKYEVDHTTGRIRLDRAVFTSMVFPQDYGSIDNTLGDDGDPLDALV
+LLPR-PTFPGVVITVRPVGMLRMVDENGGDDKILTVPAGDDRFAQLRDITDVPEHTLAEI
+EHFFAHYKEIEHGKHVTTNGWADRAAAEAVIRTA--------QNAHTRHP----------
+----------------
+>GCF_023573625_PROKKA_00062
+MAHDVTIEIPAGSRVKYEFDHETGRLRLDRVLFTSMQYPTHYGYFENTLGEDGDPLDALV
+YLPGFDLVPGCVVEARPIGVFNMTDDGGGDAKLLCVPA-DKRYDHITELEHVEESLKQEI
+EHFFTRYKDLEPGKWVKAEGWEGRAAAEAELEASIQRFDAQGEESPTDEPQGRDVDTEEA
+QPATEEGE----PQGR
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000066.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAGYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVA---GGGRG-------------------------
+----------------------------------------------
+>GCF_003691675_PROKKA_02026
+M-----------------------------------------------------------
+------------AVAVYPLAFYTSIHWAGVAIGSVVSLAS-APLASGLLERIVEYRRLSR
+WWMLAAALGGTGAALLCLSQLDQ--EAASSTATLAGVLLGLVAGATYATYSWAAHRLIHD
+GISRAASMGAVFG--AGGALLLPVLVLTGAPLIATPQAFAVAAYMALVPMFLGYVLFGYG
+LTRVPASTATTITLTEPAIAAILAVAVVGERLTPVGWTGLGIIAAVLFILALTPTNTTAD
+RHGRTPTSEAIQPALAPSPRRHNERTSPRDDAGRGSDVMWVSQTMRCQGATRPSRWEGVR
+GRFRKPYRLRPVSPDHGRATCGERTEIMRPARGLDARSVLAATMET
+>GCF_003691675_PROKKA_02194
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGRIGGAGLDPVGVALALAAAACWAAYILLSQ---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQQLTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVS---GGARG-------------------------
+----------------------------------------------
+>GCF_005280335_PROKKA_00197
+MRLIPLVLLSLLCQQLGASVAGLMFGTTGPAGMVALRLAFSALVLLVLTRPRMRTLAGLS
+RRGWVAVVMLGVTMAGMNLLIYAA--FDRIPQGVAVTFEVLGPLALSVLAN---RRWLSV
+VW---AALAFAGIALLGRDGFSA--GMDGAGLDPLGVAFALAAAACWAGFILANR---HA
+GTHLPGVQGLALAMVVGSAVAVPVGAADAGPVLLEPWVLAVGLGVALLSSSIPYGIEMQV
+LRTMPTGLFSLITCLSPVVAALTAWAVRGQRLAVLDLGGMGLV-----VLACGAAVWAAE
+RAAR--------------PSRRAPRTS---------------------------------
+----------------------------------------------
+>GCF_020097155_PROKKA_00149
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALAGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGAALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRRMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTS-
+---------------------RSPGVA---GGGRG-------------------------
+----------------------------------------------
+>GCF_023573625_PROKKA_00198
+MRLVLLVLLSLLSQQLGASVAGLLFDDVGASAMVALRVVFSAAVLLLVTRPSRAALAGLG
+PRGWAAVVGLGAAMTGMNLAIYEA--FARIPQGVAVTFEVLGPLALSVAAR---PSWRSA
+AW---AALALVGIGVLGREGFSADGGIGGAGLDPVGVALALAAAACWAAYILLSR---RA
+GTHLPGVQGLALATAAGSLVALPVGVATAGTALLSPVVLGVGLAVALLSTAVPYGIDLQV
+LRHMPTALFSLLTCLSPIAAALTAWAVRGQELTPLDLAGMLLV-----IAACAAAVWTG-
+---------------------RSPGVA---GGGRS-------------------------
+----------------------------------------------
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000068.fa

@@ -0,0 +1,19 @@
+>GCF_002008305_PROKKA_00216
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----
+>GCF_003691675_PROKKA_02209
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----
+>GCF_005280335_PROKKA_00167
+M---ENSLPAERARLGWSQQRLADELGVSRQTVISLEKGRHDPSLALAFRLAETFGTRIE
+DLFSP--DPPA------
+>GCF_005280335_PROKKA_02206
+----------------MSIDRLAEAAAIHRRTIIQIEAGRTAPRVTTLYAIAEATGTPLR
+DLLAP--LDEALERGTR
+>GCF_020097155_PROKKA_00321
+MARLARAFKVHKANSGMTYDQLAEATGLARQTLLNLAAGRTYGDLRTWLILAKVWGVTLD
+DLTAAAWRGHAGG----
+>GCF_023573625_PROKKA_00216
+M---ENTIPDERARLGWSQQRLADELGVSRQTVISLEKGRYDPSLPLAFRLAAVFGRRIE
+DLFTP--DGNAG-----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000072.fa

@@ -0,0 +1,54 @@
+>GCF_002008305_PROKKA_00250
+MTVQDPTAVAAPSPTEVFRVARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEGLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDAADAATELAPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMARYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVTL
+IDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLHR----
+>GCF_003691675_PROKKA_02262
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASSRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGGVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL
+LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGYGTEFREEDLDLQR----
+>GCF_005280335_PROKKA_00120
+MTVQDRTPADAASPTEVFRAARDLLVECQTDYERARAEFEWPRFEHFNFGFDWFDRLAQDPARQDVPALIIAEDDGRSTE
+RTFAELSAASNRAANWLAEQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSADLEDRVSRADAAWAVAGA
+EDLAKFAGVGEGLRLVHVPGVFAEGEARRAPEVPGHTVLSYDDAAGASAELSPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMDRYGVTSFCAPPT
+VWRMLIKADLAQLKTPPTKTISAGEPLNAEVIDQVQKAWGATIRDGFGMTETTLQVANTPGQKVVIGSMGRPLPGMDVVL
+IDPLTGQEA---AEGEICLRLDPRPVGLLKSYFGNQEKTDEVFRDGVFHTGDIASRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETAQSILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERSETGTAPSGYGTEFREEDLDLTR----
+>GCF_020097155_PROKKA_00088
+--------MTTTSVTERLRAARDLLVECQEDYDRARAEFEWPRFEHFNFGFDWFDQLAARPDRADVPALIISDAGGGHLS
+RTYAELSAASNRAANWLRERGITPGDRVILMLDNQVELWELMLACIKLRVVMVPTTTQMTSADLADRVERAEARWVVASA
+ENLAKFDGVDSGLHLVHIPGVAAQGDARTAPVVAGHEVLSYDDAASASPELTPDSPTPADETLLLYFTSGTTSKPKLVEH
+THTSYPVGHLTTVYWIGLQPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDAAALMADMDEFGVTSLCAPPT
+VWRMLIKADLSLLKTPPVKTISAGEPLNAEVIDQVHRAWGTTIRDGFGMTETTLQIANTPGQKLVIGSMGRPLPGMDVVL
+IDPLTGEEA---AEGEICLRLDPRPVGLLKSYYGNEEKTAEVFRDGVFHSGDIASLDESGVLTYVGRADDVFKSSDYKIS
+PFELESVLVEHPAVMEAAIVPSPDEVRLAVPKAFVTLAPSYEPTAETARQILQHTLTQLPPYKRIRRIEFRELPKTISGK
+IRRVELRKAEAERAETGQAPEGYGIEHREEDLDLKR----
+>GCF_020097155_PROKKA_02472
+-----------MSVTARLRAARDLLVEHQQDYAGARAAFEWPRFETVNFGSDWFDAVAATPERADQDALVIVEEDGTVLR
+RSYARMSADTDRVAGWLQHLGVGRGDTVIVMLDNQVELWEAMLACMKIGAVVIPTTTQLVAADLQDRVDRAGARWAIANA
+GNLVKFADVVGDCTLIHVPGVYASEAEHALPEVPGHPVHSYGDAASFAGTWSLETPTSADDPLLLYFTSGTTSLPKLVEH
+TQASYTVGHLSTMYWVGLRPGDVHLNVASPGWGKHAWSSFFAPWLAEATIFVLNFRRFDAATLMRAMDEGGVTSFCAPPT
+VWRMLIKADLTQLQAPPRNAISAGEPLNAAVIDQVQRGWGVTVRDGFGQTESTLQIANTPGQRVVIGAMGRPLPGFDIEL
+RDPQTGDRVDGEGEGEICVGLDPRPVGLFQRYHGDPEKTAEAFRDGVYHTGDIARRDEHGIYTYVGRADDLFKSSDYKLS
+PFELESVLMTHPAVLEAAVVPAPDELRLSVPKAFVTLAAGHEPGEEAARAILQHVTDRVPAYKRIRRIEFRPLPKTVSGK
+VRRVELR-AEEEQRRAGVA--GLGVEHREEDLGIRRQRRA
+>GCF_023573625_PROKKA_00250
+MTVQDPTAVAAPSPTEVFRAARDLLVECQTDDERARAEFEWPRFEHFNFGFDWFDRLAQDPARADVPALIIAEDDGRSTE
+RTFAELSAASNRVANWLSAQGLRRGDRLILMLNNQVELWEFMLACIKLRVVMVPTTTQMTSGDLEDRVTRAGAAWAVAGA
+EDLAKFAGVGEDLHLVHVPGVFAEGPARRAPEVAGHTVLSYDDADDAATELTPAEPTPADETLLFYFTSGTTSKPKLVEH
+THTSYPVGHLTTLYWIGLEPGDVHLNVASPGWAKHAWSNFFAPWIAEATIFVHNARKFDPAALMANMERYGVTSFCAPPT
+VWRMLIKADLAQLTTPPTKTISAGEPLNAEVIDQVHKAWGTTIRDGFGMTETTLQIANTPGQKVVIGSMGRPLPGMDVTL
+LDPLTGQEA---EEGEICLRLDPRPVGLLKSYYGNQEKTDEVFRDGVFHTGDIARRDENGVLTYVGRADDVFKSSDYKVS
+PFELESVLVKHPAVMEGAIVPTPDELRLAVPKAFVTLAPGHEPTAETARAILQFTLTQLPPYKRIRRIEFLELPKTISGK
+IRRVELRKAEVERAQTGAAPDGCGTEFREEDLDLQR----

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000073.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_00258
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG
+MEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>GCF_003691675_PROKKA_02272
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVASAPGMTCVGVVANGVEAVEACAAVEPDVVLMDMQMPLMDG
+VEATRRIKEAHPEVRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+>GCF_005280335_PROKKA_00111
+MHDAGHTDYSAAHIARTADGTAASGAVSAGPGGRRPGPTTPADAGRSRGSRYADRVSEDL
+RILIADDQPLMSGALRVLVSSAPGMTCVGVVANGAEAVEACAAVEPDVVLMDMQMPLMDG
+VEATSRIKEAHPGIRILAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIHAVHRGE
+SVLSPAVASKLLASIERDHPVVGPAQARPGDPDG--SDLTDRERDVLRLLARGQSNPEIA
+ANLHVSESTIKSNLTRIMDKLEVRDRVQVIIRAAQLGLVTLSLD
+>GCF_020097155_PROKKA_00079
+M---------------------------------------------------PDSPEDEI
+RVLIADDQPLMSGALRVLVDSAPGMRCVGLVADGVEAVEAVEATRVDVVLMDMQMPRMDG
+VEATRRITASRPGTRVLAVTTFSSEDYLVPALRAGAAGYLLKDAEPATVLGAVEAVRRGE
+SVLSPAVAAKLIAAVERDHPVVGPAAAEPGDPDG--SDLTEREHQVLTLLARGRSNPEIA
+AELQVSESTVKANVGRVIDKLEVRDRVQVVIRAAQLGLVTLSLD
+>GCF_020097155_PROKKA_00526
+M--------------------------------------------------------DAI
+TVLIVEDEPLLTQAYTMILEADPGIRVVGTASDGAAGVAEHERLRPDVVLMDLRMPVLDG
+VEATGRIMREHPEAKVLVVTSMTTEDYLSPALANGAAGYLTKDTDAEGLVRAVRAVEAGT
+MALGPSIAREVVDLLLRSG--VAPRTDAPASPRDLPEALTPREQDVLELLAEGLTNQEMA
+ARLYVSDSTVKSNLARVMHKLGANNRVQALVLGVRAGLVSIP-G
+>GCF_023573625_PROKKA_00257
+M-------------------------------------------------------SEEL
+RILIADDQPLMSGALRVLVDSAPGMTCVGVVANGVEAVEACAAIEPDVVLMDMQMPLMDG
+VEATRRIKDTHPAIRVLAITTFTSEDYLVPALRAGAGGYLLKDAEPPAILGAIQAVHRGE
+SVLSPAVATKLLASIERDRPTVGPTSVQPGSPDG--SDLTERELGVLRLLARGQSNPEIA
+ANLFVSESTVKANLTRIMAKLEVRDRVQLIIRAAQLGLVTLALD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000075.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_00282
+MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSSSMVGLGWITGRATGLPWWASAMVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---
+>GCF_003691675_PROKKA_02297
+MT----------GG-----------------DPAALMDALGAWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRTLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGSMVGLGWLTGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---
+>GCF_005280335_PROKKA_00071
+MTVLTPAWFAASGGVPTMGAGAAAASGAGAWDPSALLDSLGAWFHPLTALLVALDAPI--
+PPVPSEVFVIGSGALAAEGRVGLAAAVLTAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRVHRGIRVLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGWMVGLGWLTGRTTGLPWWASAVVGMVFGTLAGLIIAGVVA-RRRARKG-------
+---
+>GCF_020097155_PROKKA_00057
+MT-----------------------------DVTALLEGLGPWFHPLTFLLVALDAPV--
+PPTPSEVLVIGSGSLAAAGRLGLATSVLTAWLGCWAGD-VGLYALFRHRLTSVLD--RWG
+WGRAVHAGIRRLMEKAGPASSLAGLFVLRFVSGGRTASMAAAGVAGVRWRPFLWLSGTGS
+LAWSVYMVGLGWITGSATGLPWWASAVVGVVLGTLLGAAVAAVIAWRRRGKEGA------
+---
+>GCF_020097155_PROKKA_00450
+MPVLTNIL-----------------------DAASILHSLGPWTLGGIGSMVFIESGVLF
+PFLPGDSLLVTAAALHVELGIALWAIILVAGLAAILGDQVGFYLGHRYGRRLFKDDARVL
+KTERLAQA-EAFFERRGPLALVLG----RFVPIVRTYVPVAAGTAGMPYRSFVGWNIGGA
+VAWVCSMVAVGALLGQIPGITKSIDGIMILIIVISVAPIAIQALRARRKARRDAVMTEGQ
+PVA
+>GCF_023573625_PROKKA_00281
+MT----------GG-----------------DPAALMDALGVWFHPLTALLVALDAPI--
+PPVPSEVVVIGSGALAAEGRVSPVAAVLAAWLGCWAGD-VGLYALFRHGLADRLD--RWA
+WWRRIHRGIRSLLVRVGPAGSLAGLSVLRFVSGGRTASMAAAGIGGIRWPVFLWLSGAGS
+LAWSGSMVGLGWITGRATGLPWWASAVVGMVFGTLAGLMIAGIMAHRRRGRKG-------
+---
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000078.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_00310
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSTLVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLTAVGARVLGTAGGPEKVALGRGLGAEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVTDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA
+>GCF_003691675_PROKKA_00025
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPTGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGTEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA
+>GCF_005280335_PROKKA_00027
+MSETTRTPGTGRGTMRAVRFTGEGGAGSLAVGQEPIPTPGPGEVLVKVAAAGLNRADVMQ
+-REGKYPPPPGASDVPGLEVSGVVVALGEEAGLPGEGRFAPGDEVCAL----LAGGGYAE
+HVVVPAGQLMAVPPGVDLVTA------AALPEVACTVWSTMSERGGVRAGDVVLVHGGSG
+GIGTFAVQYLAAIGARVLATAGGPAKCERVRGLGAEDVFDHRSGEPGAFADWVLERTGGR
+GADVVLDVVGGPYLDANVRCLAEEGRIVVIA--VQGGPKADGFNLMRLVSKRGWLTGATL
+RARSVVDKARIVAGTERAVAPLVAAGRIDLAVGARFPLDDAAAAHRRFEAEDRVGRVLLV
+TDPADALWPQEDRT
+>GCF_020097155_PROKKA_00023
+MD----TA----PDMLAVRFAGAGGTDVIRVGREPVPEPGPGEVLVRVAAAGLNRADVVQ
+-REGHYPVPPGASEVPGLEVSGTVVALGPQAGVAGEGRFAVGDRVCAL----LAGGGYAE
+HVAVPAGQLMSVPDGLDLVSA------AGLPEVACTVHSNLEGRAGVRPGEWALVHGATG
+GIGAFAVQYLSAVGVRVLATAGGPAKVARALELGADAAFDHRAAAPGAFADWVREITGGH
+GADVVLDVVGGPYLAPNVKALAMDGRIVVIA--AQDGPVPEDFHLMRLAARRGWVTGSLL
+RPRPPDEKAGIVAAAERAVWPLVAAGRIDPGVTARFPLREAAAAHAHFEGAARMGKVLLV
+TDDADALLPGG-AA
+>GCF_020097155_PROKKA_00654
+MHPS--LP----RTMLAAIIPAPGGRPELR--QCPVPEPGPGEVLVRVMASSVNPTDVMT
+WRRGMFVTGQTVPFVGGYDMSGIVVKLG-----RGVTALDVGDAVTGMPRFPAPAAAFAQ
+YSAVPARHLARIPTGTEDLSAGAWGRWAGLPLAGLTAYQALVDTAHLQSGQTVLVHAASG
+GVGSLACQLAVNLGAQVTAVTSDRGR-TLVEVLGTRHVVDR------ATVDW--QRFAG-
+CFDVVLDTVGGDTTPRSLAMASPDGVVVALHPYAHDDLAQRDPRLRRMLVE---------
+-----PDHHALELLIEQA-----ARGRLTVQVGAGYPLSDLGDALLHVETNKTPGKTIIH
+I--------QGDNA
+>GCF_023573625_PROKKA_00317
+MD----VP----AQMRAVRFTGAGDNGVVRVGHEPVPDPGPGEVLVHVAAAGLNRADIAQ
+-REGRYPPPRGASEIPGLEVSGTVAALGPEAGMPGEGRFAVGDRVCAL----LAGGGFAE
+YVAVPAGQLMAVPDGVGLVEA------AALPEVACTVHSALVGRAGVQAGDRVLVHGATG
+GIGSFAVQFLAALGARVLGTAGGPEKVALGRRLGAEHMFDHRAAESGAFAPWVKEVTDGH
+GADVILDVVGAPYLAPNVSALAPEGRIVTLA--VQGGAVPEDFNIMKLVVKRGWLTGATL
+RSRSVVDKAGIVAAAERAVWPLVAAGRIDASVGACFPLAEAAEAFDWFDSATRTGKVVLV
+TDPADARRPSGDRA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000084.fa

@@ -0,0 +1,54 @@
+>GCF_002008305_PROKKA_00418
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR
+LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR
+PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ
+HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTQQNDADGAE
+RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS
+STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL-------
+AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R
+>GCF_003691675_PROKKA_00139
+MPQSTLYWIIAAIIVVLLILIIVSVIASRRRREAEAEAAETRLERR---------GV---SADTAGEQAAAPAAPTRLSR
+LDEVAAEKDARPAPAVRPAGGLAA------------FDTAAADRETDESGA--GVAGGAGVTVDQQDAPSTEATAQTHRR
+DAA--APATRGTLRPAPAVPSTVREADTVGLGAAGVAGGSGVTLDEQTPAADVPATPASPSPVTETPA--PAAPVAEAPQ
+QRSHLTP----APEHVHGTVPADEVAAEHTPTKEFATDGIPVPQGEHLETHTVATTAHGSVTVVATESDQAQQTGVDGTE
+RSAAGSLRIDGTPGVPGRVAEADREPARTDD-------------HGADVAQPAAVEPAAERPPLEAA---------PATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAA-------AGTAGTAAPTS
+STPTTVAPDT--------STSSAPTDEEPAEDDTEGAALPDLRADRDE-------------TRASDAEGESKL-------
+AQAGAVAASAFETVRDKVAVPLRDNVAVPAK--DKVVKVVKDKLSQAQERRWGK--------------R
+>GCF_005280335_PROKKA_02541
+M-------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+-----------------------PTDAEPAADDTEGAALPVQDATRADAVRP-------GTARTDASAGDSKL-------
+AQAGAAAGTVLETVRDKVAIPLRDNVAIPAK--DKAVKVLKAKLAEAQERRRNK--------------R
+>GCF_005280335_PROKKA_02542
+MGESTLYWIIGAIIVVLLILIILSVVASRRRRAAEAEAAEAQLERR--RVTPTAAGVGASHEDALEETHDADARPHTVA-
+----STGGDVAPAAAAGAAAGTTRLSQLDDVA----PVAAAAADADAESLPADGVAAGSGVTVDQQ-----DASDQS-VR
+PAAPAAPAGADTRGPNASVKSAGAAAAAVGLGAAGVAGGRGVTVDQQDAAADVPSTPASPSPVAQTPAAPSSAGATTAQD
+DRADRTAQDAADAEPVKGTVPLSEDAHAVPPAADPPSGGDAVADDAHLEAHTVATTEHGSVVVVTAEQDEDDQATA----
+--------------------------------------------------------------------------ASRETE
+--TETDDSRG-----DDAGQDRDAERAVAEGVAGGTGVTVDQKAV--------AEAAATQGAPASAAGAASAAGAAARRR
+DRGRRLDPACGGARLLQDRRH--AGHARPRRLRGAGRGRG---GDR--PARPPRRRP-----------GDARLHHPRDAP
+GRRAG------------AGPGRRRRGLPQGRGRDPAAPPRGRRPGAKPRRRPTSTRPRPRPPRRTAPAR
+>GCF_020097155_PROKKA_02410
+MPQSTLYWIIGIIIVVLVIILIVSSLRAKRGREEEAAAAGRHADSAPAPLAATAARGGTVGASTVPATGDAPADRTDGR-
+----AAGATALPSFDVDEVDRRAAEQREQDVVERRRATGAEAGAAGHAAVP--GVTGGSGVSVDEAEGVAKDATGQD-VT
+PVA-------DAQRRNGSSAAPAATGAGLGLAAAGVAGGTGVTVDDAGTGADLPAPKGSPAGVVEVAE--TQAEAAQA--
+--------DAAPAEHT--VVP-------------------GVAGGDAVTVDTADVQSSSAPQGAQAAAGRSDLTDAE---
+---ARTYPVTGLPGVPSAVDPEQVAAARVQDAAELKAAEGQGAEHERGASQPADPESVPGTVPLTGE--EAVIEAPVHTH
+--EMPEPVLGTPAYIQDSTTGQDPTEDLPEGQVYGTTPLSGEDAIVEPADQLPAEAAETEDRAASDAGTASAETAVVPVE
+ETETAVVPVA--------ETR--SADAGPSEDSVALTGQGVETADRVEPAAPVAGTPARDEARTHD-EHRSRLEIVKDAV
+AETAGTVATTAGTAAEKAAPVVRSAARTVGKAAGSAASTLKDKLAQAQERRWGK--------------R
+>GCF_023573625_PROKKA_00421
+MPESTLYWIIAAIIVVLLILIILSVIASRRRREAEAEAAETRLERR---------GTTADTADTAGEQAAAPAAPTRLSR
+LDEVAAEQDARPAAAVKPAGGPAA------------SETAAAGRETDESVA--GVAGGAGVTVDQQDAPRTDATAET-SR
+PTA--APTTRGTLRPAAAAPSTAREADTVGLGAAGVAGGSGITLDEQTPAADVAAAPASPSPVTETPA--PAAPAAEAPQ
+HRSHLTP----APEHVHGTVPAEEVAAEHTPTKEFATDAIPVAQGEHLETNTVATTAHGSVTVVAAESDQTRQNDADGAE
+RSAAGSLRIDGTPGVPGRVAEAGREPARTED-------------HRADAAQPAAVEPAAERPSLEAAAERPSLEATPATR
+RAEAPETHAG--------TTPATPLGGAPELDPTAASSGRAEDAT--PATRREARAAQSAAAAGTAA-TAGTAGTAAPTS
+STPTTVAPDT--------STSSAPTNEEPAEDDTEGAALPDLRADRDE-------------TRGSDAEGESKL-------
+AQAGAVAASAFETVRDKVAIPLRDNVAVPAK--DKAVKVVKDKLAQAQERRWGK--------------R

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000086.fa

@@ -0,0 +1,55 @@
+>GCF_002008305_PROKKA_00448
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG
+>GCF_003691675_PROKKA_00169
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAISLAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFRG
+>GCF_005280335_PROKKA_02509
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDTKRYLGKGVLDAVAAVE-EIADELEDEFAVDQRAVDRLMLD
+LDGTPNKGKLGANAILGVSMAVAAAAAQSSDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHSLKKVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVEKAGYTLGED-IALALDVASSEFCE-KGAYTFEGQKRSAEDMVAYYTE
+LADNYPIVSIEDPLDENDWDGWRLLTEKLGDRVQLVGDDLFVTNVERLQRGIDDKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRYRG
+>GCF_020097155_PROKKA_00683
+MNDYISGIHHHGAHQGEYVTHHDHPVTIDAVHGARILDSRGYPTVRVSLELDDGRTVTGD
+APAGASTGAHEAVELRDGGSA-FGGRDVTQALHLIDTDISGLLTGRSWSAIGQIDAALAE
+LDGTTGYRRLGANSVVATSIAASRALAHAADLPLWQWIAEITGSTPRMPVPHFNVLNGGA
+HAANELDFQEFMIAPVNAGSMADAVRIGADVYHALAALVRDRFGSLGLGDEGGFAPSIAA
+PEEALDLLVDAIRTAGYEPGVDQVAIALDPAANEFSQGDGSYRVLNDSLDRDGLVDYYRH
+LIDTYPIRSIEDAFAEDDHEGFRRMQAALGDRIQIVGDDLYVTDPQRIRDGGEQQLTNAA
+LIKPNQIGTVSQTLGAIATAKSIGMASMVSHRSGETTDTFIADLVVGTGTGQIKSGAPGR
+GERVAKYNRLTEIAEQ---------HPELPYGLI
+>GCF_020097155_PROKKA_02380
+M------------------------AQIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDTERYLGKGVQDAVNAVF-EIAEELEDELATDQRAVDQMMLD
+MDGTENKGKLGANAILGVSMAVAVAAADSADLPLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRMGAEVYHSLKKVLQEKGLSTGLGDEGGFAPNLES
+NRAALDLIAEAVQKAGYTLGED-VALALDVASSEFCE-NGSYTFEGRQRSAEEMSAYYAE
+LVDAYPIVSIEDPLDENDWEGWEHLTEQLGDRVQLVGDDLFVTNVARLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLADAAVYAGRSAFPRFQG
+>GCF_023573625_PROKKA_00451
+M------------------------ALIDAIHAREILDSRGNPTVEVEVLLTDGSLGRAA
+VPSGASTGEFEAVERRDGDKKRYGGKGVLDAVAAVE-GIAEELEGEFAADQRAVDRAMRD
+LDGTPNKGKLGANAILGVSMAVAVAAAQASDLMLYKYLGGPNAHV--LPVPMMNILNGGA
+HADSNVDIQEFMIAPIGAPSFREALRWGTEVYHALKTVLQEKGLSTGLGDEGGFAPSLES
+NRAALDLIAEAVTKAGYRLGED-IALALDVASSEFFD-NGSYTFEGQQRSAEEMAAYYTE
+LVDNYPIVSIEDPLDEDDWDGWQHLTAQLGDRVQLVGDDLFVTNVERLQRGIDEKAGNAL
+LVKVNQIGSLTETFDAIALAQRHMFHCMISHRSGETEDTFIADLAVATNAGQIKTGAPAR
+SDRVAKYNQLLRIEEDLDDAAVYAGRSAFPRFRG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000090.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_00521
+MTPRGSCWSSLPVGARFRLWNTLDPMHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAARKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGADGEKNNREVVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q
+>GCF_003691675_PROKKA_00243
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVA-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVRATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q
+>GCF_005280335_PROKKA_01219
+-------------------------MRFVVTGAGGFLGSNVVRELLAETDHDVVAVSSQT
+DRELAAQLERAPYPALRRFPQVHPRTRL-LEAG----------FLRDGDIVINCAFPWNR
+GGRAMADGLEYLTR----LFQSAHAVALH--TFVNVSSQSVYSQARTEAA---DESSPVE
+CDTPYSTGKYAMELAAELVLPPKVLVNARMSSLIGPGYDVRIVNRFIARFLAD-----EP
+VSIQGGDQVFDFMDVRDAARALIAVALAGPPEGSAALNIGSGAPRTLRDIAQTVADVVRT
+HTGHDPRIAWEPSAGDDRTLGLDSGLLRREYGFAPRHTLEDSALS---------------
+---ILQAMTSAQSASVGETPTGSVEGGRR
+>GCF_005280335_PROKKA_02428
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAQSDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEAKYRAAG---------------Q
+>GCF_020097155_PROKKA_02311
+-------------------------MHLLVTGGAGFIGSNFVHHVVRETGHDVVV-----
+-------LDKLTYAGNRENLAGLPEDRVTLEVGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGQGINVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNKEIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPQFTDIRAGLADTVRWYRENEAWWRP
+AKDAVEATYRAQG---------------Q
+>GCF_023573625_PROKKA_00521
+-------------------------MRILVTGGAGFIGSNFVHHLVRETDHDVVV-----
+-------LDKLTYAGNRDNLVGLPESRVRLEIGDICDAALVDRLVAESDAVVHYAAE-SH
+NDNSLNDPSPFIQTNIVGTFVLLEAVRKHGKRFHHVSTDEVYGDLELDDPAKFTETTPYN
+PSSPYSASKAGSDHLVRAWV-RSFGVQATLSNCSNNYGPYQHIEKFIPRQITNLIDGVRP
+RLYGHGVNVRDWIHTEDHSSAVLRILERG--EIGRTYLIGSDGERNNREIVEILLELFDR
+PADDYDLVADRP--GHDLRYAIDNTALRTELGWEPRFTDIRAGLADTVRWYRENEAWWRP
+AKAAVEATYRAQG---------------Q
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000092.fa

@@ -0,0 +1,31 @@
+>GCF_002008305_PROKKA_00554
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+>GCF_003691675_PROKKA_00279
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+>GCF_005280335_PROKKA_00640
+MERPAPTA-------EICPVRPEDTDAVVALWERTLPEY--GDPTRPQRAPRPSIRRKLD
+-WGDGLFWLAVSDEEVVGTV--------MAGYDGHRGWIYS-LAVHPDHRRGGLGTALVA
+H-AEQELARLGCPKVNLQVLATNADGAEFWAATGYQPDPVLG------------------
+-LGKRLG-G
+>GCF_005280335_PROKKA_02391
+MTETAPTVPTPPARPQVRPLRPEDHEAVAAL---TVASYVDGGHIAPGSRYVKTLRDVAG
+RAARAEVLVAEVDGQVAGSVVLTPLGSPMAETAAPGEYEFRMLAVHPDHHRRGVARTLMA
+VIEERARALPGIEAIALTTMPTMTDAHRLYEALGYVRVPERDWYLRDVIPDLDPADETGP
+FLVYRLPLA
+>GCF_020097155_PROKKA_02275
+MSDVT-----------VRALRPEDHEAVAAL---TLASYTTGGHFEAESDYLETLADVAG
+RAAVAEVLVAELDGQVAGSLVLTPHGSPMAETSVPGEYEFRMLAVDPAVHRRGVATALLA
+EVVRRARATPGVEAIALSTMTSMTDAHRMYERLGFVRVPDRDWRLSDLEPGLDPAEDAGP
+FLVYRLPLT
+>GCF_023573625_PROKKA_00557
+MSAL------------VRPLRPEDHEAVAEL---TLASYVDGGHIAPDDAYVKTLMDVAD
+RAGRAEVLVAEVDGEVAGSVVLTPPGSPLAETSGDGEYEFRMLAVHPRFHRRGVGGALLA
+EIVARARAEEGVDAVVLTTMPSMTGAHRMYERAGFVRVPERDWFLADVVPDLDPADETGP
+FLVYRLALD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000098.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_00626
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSAREWSDAHAANAVLDAHAGDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVRVRCCHWFRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLALDALQMALARR
+GGKAEVQGCRVHSDRGSQGGFNR--SSQHPLGITGGMGD-GKQG----------------
+--------------------------------LGE---------------EDQ
+>GCF_003691675_PROKKA_00371
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLRKLTPVEFEMVQSVQAAAAA
+>GCF_005280335_PROKKA_00392
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALARR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQAPLGRLTPVEFEMVQSVQAAAAA
+>GCF_005280335_PROKKA_00411
+MTYPVVKDLARDGIPVRLCCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFR
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFLKR--------------------------
+--------------PGSD------------------------------------------
+--------------------------------------------------EDS
+>GCF_020097155_PROKKA_02188
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYPWLAEPVSAREWSDAHAANAVFDAHADDP
+EFGYRFLADELRGRGLDVSDHQVLKACRLVRVRCCHSIRRGSGKRPGPAVHDDLVRRQFR
+ADKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSIDRRMSSQLAVDALQMALARR
+GGKAGVQGCRVHSDRGSQFRARRFVETLRVNSLIGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWDSFAQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+>GCF_023573625_PROKKA_00605
+MTYPVVKDLARDGIPVKLSCRVLGFSRQAYYQWLAEPVSEREWSDAHAANAVLDAHADDP
+EFGYRFLADELRGRGLAVSDHQVLKACRLVKVRCCHSIRRGSGKRPGPAVHDDLVRREFA
+AEKPNQLWLTDISEHWAGDSKLYLCAVKDVFSNRIVGYSINRRMSSQLAVDALQMALGRR
+GGKAEVQGCRVHSDRGSQFRARRFVETLRVNGLVGSMGRVGAAGDNAAMESFFALLQKNV
+LNRRRWQSFDQLRLAIVSWIERTYHRRRRQARLGKLTPVEFEMVQSVQAAAAA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000100.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_00644
+M-------------TSVPTV-----PFHDGQQIPQLGFGVWKVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK
+LGTDYVDLYLIHWAKPAQGKYLETWKALIEAQKQGKVRSIGVSNFPAAQLEEIIEATGVV
+PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA
+QVVIAWHLAHGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV
+IDF--
+>GCF_003691675_PROKKA_00381
+M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDVSLDK
+LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKRGKVRSIGVSNFPAAQLEEIIEATGVV
+PVIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEVRGATPA
+QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTDDDVARIDALDREDG-RLGPDPAV
+IDF--
+>GCF_005280335_PROKKA_02319
+M-------------TSVPTV-----PFHDGQSIPQLGYGVWRVEDEVAADVVAQAIRAGY
+RHIDTAAIYGNEEGVGRAVAAS----GVPREELFITTKVWNSAHGYDEAL-AALEESLGK
+LGTDYVDLWLIHWAKPTQGRYVDTWKALIEAQRQGKVRSIGVSNFPAEQLEEIIEATGVV
+PVIHQVETHPYWQQRELRELEERHGILHESWSPLGQGGELLE--DPEITAIAEAHGATPA
+QVVIAWHLAKGFVVIPKSVTSERIVSNLAAADVELTEDEVARIDALDREDG-RIGPDPAT
+IEF--
+>GCF_020097155_PROKKA_00584
+MSTDSRHTAIPVDETPVPETLTLTGTGVDGVEMPRIGLGTWPLRGAEARDAVEQALRIGY
+RHVDTAQNYGNEDAVGEGIAAAIHAGVLDRDQLFVTTKVNREHHGDARTVRAAVECRLRV
+LGLEHVDLVLVHWPNPDQDRYLETAWSLSELAEDGRIRAWGVSNFTPAHLDRLAGAGLRA
+PV-DQIEVGPLRQSPAWQEGVRAHGAAITAYSPLGRADQDLGALEP-VAAAAARTGRTPA
+QVVLRWHLQSGRAAVPKSVDPARQAQNLDVFSFALTAEEMAAIDALDTGEGPRRHPD---
+-EFGH
+>GCF_020097155_PROKKA_02178
+M-------------TTVPQT-----PFRDGQSIPQLGYGVWQVEDAVAADVVEQAVRAGY
+RHIDTAAVYGNEEGVGRAVAAA----GVPREELFITTKVWNSDQGYDEAL-AALEASLAK
+LGTDYVDLWLIHWAKPAQGKYVDTWKALIEAQRQGRARSIGVSNFPAEQLEEIISATGVV
+PVIHQVETHPYWQQRELREVESRHGIVHESWSPLGQGGELLS--DPVITAIAEAHGATPA
+QVVIAWHLAEGFVVIPKSVTPERIVSNLTAAELELTAEEVDQIRGLDRADG-RIGPDPAS
+ITF--
+>GCF_023573625_PROKKA_00614
+M-------------TDVPTV-----PFHDGQQIPQLGLGVWQVEDDVAADVVEQAIRAGY
+RHIDTAAIYGNEEGVGRGIAAS----GVAREELFLTTKVWNSDQGYEEAL-AALDASLDK
+LGTDYVDLYLIHWAKPAQGKYLDTWKALIEAQKQGKVRSIGVSNFPAAQLEKIIEATGVV
+PAIHQVETHPYWQQRELREVEGRHGIVHESWSPLGQGGDLLA--DPVVTEIAEARGATPA
+QVVIAWHLAQGFVVIPKSVTPERIVSNLEAAGVELTADDVARIDALDREDG-RLGPDPAV
+IDF--
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000104.fa

@@ -0,0 +1,126 @@
+>GCF_002008305_PROKKA_00731
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP
+DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP
+RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADALVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR
+Y------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--ADDGDGTLTPPGQVGARDAVDGLTVTLARSGD
+-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDAEGA--GEAAL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>GCF_003691675_PROKKA_00462
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGRRSVTYAEGVGSAP-----ARGPELAVVTEHGP
+DAGRIVPLGEGGLSVGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRATGRLWDGRSPLPVGRTALGLVRGPGSALP
+RPITPEPPVVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPMFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADAVVRRR------------ARVALSPGAVARAVRSGATDRF-----------------------GLTAG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRIWWSGGSGPQLLVMAPEDAA--LDPAWRAWRAAIGDDA--GTTPT-ARTDLPWTR
+Y------------------------------------------------------DFTGPPPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDMAADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVALARSRD
+-EAGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GAASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVENYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVAMRSGRP----VAVLDGTGEAAT-AARS---------GTPVLTPDSEGA--GEAVL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPAAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLVW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>GCF_005280335_PROKKA_02222
+MGWTVRILGGRTPETWRVSPLPRDPTLRDRAVRERAPGRSLRAVASGPGSVTYAPWGGAEP-----APGPELSVVTERGP
+DGGRLAPLTGGGVSVGRGRARLLLDDPAAPSRPTRLRLAAAGLHVEGAVEGAPRLWDGRRPHRIGRTTLGLVRGPQPPLP
+PPSLPAPPCVDLGSPPAGQSLAIPLLTAAAPLVIGVALVLVMRNPIFLLFGLLSVAVALTMLGLQRRARMRHAALLAE--
+-RAAAVTAHR------------ASAALSPGDVARAVRARTPDRF-----------------------GLTGA-AEGPAT-
+------LSWGLGMGALGLSRDD-----PDQAWVAAVTARREALTVPSPAARTVVLG-----PPR--------EAAGVCRW
+VVFQLLRHAVAAGACLVVESGGSRRCWWAGGTGGALLVTAPADAA--LEAAWTAWTAGIGG------APG-ERTGAQPAR
+I------------------------------------------------------DFTGADCAPGET-VVDLRGGMLTDP
+GQEQRI---------TGLEADGIAPATLPGWAAELADDVVDLGLLP--ADAGAGALFPPADVGTRDAVDALRVSLEAGSD
+GGPGALALDLAAD---GPHLLLAGTTGSGKSDLLLSLLLGVAAHHPPAEAAFLLLDFKGGASFGPLAALPHTMSLETNHV
+GAASL--RALNAIRAELHRREALFAEAG----VSDYPAFRRRH-----PEAALPRLVVAVDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLVLATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAATRLDPRRPGSAILSTAGREPVPFRASR
+------------------WAVDGGAPVWRR---LG-----------EAAETPAAAPW---------KAVVAQLVERYAAG
+RWPTP-PPVVTPALPERWVPDRTRRAGATA---------------LALLDDAAHGRHRPWRWAPGGGGRAAWIVE--PAG
+GRAEALAAVLEVGVRGGAP----VVVLDGTGEAAAIAAPE---------GVRLLRPDEEGA--GERAA------------
+---------------ACLRELAAAGGTAVLTGWTTWAGLRLGESYRTLEEDAQGWLGGREAAGLRVAAFGGRE-LATSRL
+LLHLPHRFFVPAGTSAEHRLVW-PRLVEV-EPLPGRAVHVSPDVPEPGLPC--QLASPGAHRSGAADAASTL--------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------
+>GCF_020097155_PROKKA_00342
+MTRRL-----------------------------------VHR-----------------P-------------------
+--GRTVP-----------PARLLPED--------------------------------------------VITGPQ----
+----PVDPAMDQGSGP-NLLMIVPMVAAAASMLTMMAFRQSPFAAVGALAMVVTLTAMLILYGSQAGKARRRRTTLRETY
+TRYLDRQRRRLIAEDEQARAIAASAAPPPGALLDVVR--RPDRLWERRRTDEDFLQTRVGLGARPVRALRVA-VQDNATQ
+VQDEFMLKQAESLATRFRTTDDMPVSLPLDSLGNLAVVGPREFGLTA--ARSLVLGACVQQAPEDLVVALLVPPERRADW
+PWFDRLPHARVADAA--------------SPTGNRLLVAADADDLMRMLRADLARRAGIAAETLRASTRD-GRAATELSR
+LVIVVDSHGEPAAGLPLEGSHLPLVSRGITLITLVSDRLDEPSDVRLRLSATGGTDVTGAAEFQVDD-ARQDEGRPTVSH
+GRLDTFDAATALGVATDLQPLRLSADSLEHAEDDLSSTQTFLQMLGLSPELTLEELRRRWRPRGQDEF--LRVPIGEDDR
+GDAVHLDLKEAAQLGMGPHGLCVGATGSGKSELLRALVFALLASHAPERMSLLLVDFKGGATFAPFHGAPHVAGIITNLS
+DDLSLVERVYASLSGEILRRQEVLKAAGNLANITDYQVHRERELAQGRSVEALPHLIVIIDEFGELLTARPDFIDLFLSI
+GRIGRSIGVHLLLSSQRIESGRLRGLETYLSYRLGLRTLSESESRTVLDTADAFHLPP-LPGFGYLKVDTSVYTRFRSGY
+VSSPLEEEAAARAEQERVLTADDDVPPALPVPDYGLQLVLPTEGAEPQLSSGAGAAQVMEEPEDHRPTIMETLMD--RLR
+EVPSPVEPLWLPPLPEALTLDQAAGDVAVTDHGLRLPAGGDLEVPIGLIDDPEHQWQGLWMLDF-ASGSGHLIVQGGPRS
+GKSTLLQTIVTSLALTHSPQQVGVYCVDLLGSSLL-PLQG----LPHVGGVAIRTNREMVTRTLREVSAMLTLREKLFEA
+EGIDSMTTLRRRHADGSLPDLGSADVFLVLDGYG-----QVNEEFADLTPVLNGLISRGAAYGIHIITTVARQGEIRSTQ
+QTFFTHRVELRLSTPSDSAIDR-KAAEEVREDTPGRGLASTRLHGQVALPRVDGAADPGTAAEGLAETVQRIAESARGEA
+MAVRVLPPTTERPPLEQLEDPGRLPVGLLEDDLSVRSLDIDGRERHVVALGDAQTGRSSMLRQFARHFMDTHADTEMMFV
+VFDPRGELKGVIPDAYMAGYAGNATVAVPLARALVSELEKRQSTDPKDAGPMRQARIVVLVDDYDVLTVAGDSPLAPLLP
+YLPMARELKLHVFLTRRMKGASRGLYEKFLASLVSQDAVTLMFSGDRSEGVLFDGLRPKRLPPGRAVLIGASRRHETVQT
+FTGPPAPGRG
+>GCF_020097155_PROKKA_02098
+MTWRVRVLGLPVEQDWAVSELPLDVDGQDRVVAEHFAPLRVERARGGGTTLTYVAHPSGTPPVPAAGSGPELAVGTSAGP
+DAGRLVPLTAAGLTVGRGRSRMLLDDPQCPSRPVRLALGPSGVSVDDG--RTRRTWDGLDGLPIGDSILRLVRGRQRPLP
+PALTPPPAQIDLGAAPAEQSLLVSLAMAVGPVLIGLVLAVTTRSPLFLLFGIVSLLGVGVLLGVQRRTRRRHADLLRE--
+-RALDVVRRR------------VAAVSGPADVSAACRAKAEDRF-----------------------GLVSARPGDGPA-
+------LLWGRARGSVAFTRGD-----VADHWRSAACVDQPVLGVAAADRGTVLCG-----TGR--------PAQAAARW
+TLFQLLRHAVATGSSLVVRSPDGARVWWPAVPGAPTIALELEDTA-PLAGAWEVWTASLGAEM--SETRRHGCADEVLVR
+--------------------------------------------------------CTGTPPADLDADVVDLDARQATLP
+GQGLEL---------TDLTPLGISADTLQWWLAELADDVAHLGLGG--PPASAPPLRRPHDVGAHRAVRNLAVPLTSSSA
+GDAAPMVLDLAAD---GPHALIAGTTGSGKSDLLLSVLVGLAARHAPAEVSFVLLDFKGGASFGPLRRLPHTMSVETNHV
+GAASL--RALQAIGAELRRREALFAEAR----VADYPAFRAAH-----PDTALPRLVVAVDELRVLVDEHPDANAVLQRL
+AATGRSLGFHLLLATQRPGGAVSADVRSNLGTTIALRTATEQESWDLVGSAAASRIDPAAPGTALLARGTGAPVPFRASP
+------------------WSAGPVRPRWTP---WGV----------PVASAASGTDW---------PSVVEDLVQACRDR
+DLPIP-EPVVSPPLPGSFAPDRSRRRSADV---------------LALVDDAARARHVPWRWPLGAQGNGAWIVE--PAG
+GRALVLAAVLEAAGRTSPA----VLILDGSGECAA-ALPTVADALPDLADVTLLTPEAQPADVGEQVC------------
+---------------GAVADLAAVGGTLVITGWQSWAGVRVGETYRTLDEELHRLLGTQAARGLRVAAVGGRE-LVTARI
+APHLPHRFYVPAGTTPDHRLVWPPKLVEV-EQLPGRAVHVHPGGPTVGVPA--QLAFPAHSAAGAGTDSDDQ--------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+---------Q
+>GCF_023573625_PROKKA_00695
+MAWSVRILGGAAPETWRVEHFPADADEQDRAVRERFPARSLHRCAAGPRSVTYAERVGSAP-----ARGPELAVVTEHGP
+DAGRLVPLGEGGLSTGRGGARLLLDDPSAPSRPMRLRLAPTGLHVHDGPRDTGRLWDGRSPLPVGRTALGLVRGPGAALP
+RPVTPEPPAVDLGSPPARQSVVIPLVAALGPLVLGVALVLMMGNPVFLLFGVLSVTVALVMLAMQRRTRLRHARLLAA--
+-RADAVVRRR------------AQAALSPGAVARAVRSGATDRF-----------------------GLTSG-ADEAVA-
+------VSWGSGVGALSLSRDD-----PDEAWVEAVTSRRTVMTTSPPESRVVVLG-----PPR--------DVAGACRW
+AVFQLLRHAVAADGAFVVEAGGVRRTWWSGGSGPRLLVSAPEDAA--LDPAWRAWRAAIGGDA--GTTPT-ARADLPWTR
+H------------------------------------------------------DFTGPSPAPGDA-VVDLRGRTVVVP
+AEQQRF---------EDVTADGLADGTLVAWLTELADDVVDLGLLP--TDDGDGTLTPPGQVGARDAVDGLTVTLARSGD
+-ETGVVEMDLAAD---GPHLLIAGTTGSGKSDLLLSLLLGAAAHHPPAEVAFLLLDFKGGASFGPLGALPHTMSLETNHV
+GTASL--RALSAIRAELHRREALFAEAG----VSDYPGFRRRH-----PDAALPRLVVAIDELRVLVDDHPDAAAVLQRL
+AATGRSLGFHLILATQRATGAVGSDLRSNLGSTIALRTATEQESWDLVGTAAAARLDPRRPGSAILSTAGRPTVSFRASQ
+------------------WTVDGGTPVWRR---LG-----------EAAAAPAVAPW---------EAVVSVLVEKYAAG
+DWPTP-PPVVTPALPERWVPDRARRAEATA---------------LALLDDAAHGRHRPWRWPTGAEGRTAWIVE--AAG
+GRAETLAAVVEVALRSGRP----VAVLDGTGEAAA-AARS---------GTPVLTPDVEGA--GEAAL------------
+---------------ARLRELAAAGGTAVITGWNAWSGLRVGDTYRTVEEDVHDWLGRPTAAGLRLAVFGGRE-LATGRL
+LLHLPHRFFVPAGTNAEHRLIW-PRLTEV-EPLPGRAVHISPAVPEPGMPC--QLASPAPA-------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+--------------------------------------------------------------------------------
+----------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000105.fa

@@ -0,0 +1,25 @@
+>GCF_002008305_PROKKA_00747
+------------------------------------------------------------
+----------------------------MLSGFCLALGTWSTVAAEAADAALARRWGAAA
+RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>GCF_002008305_PROKKA_00748
+MSGAGYEVFALFQVALLACLAAGGVLGALARRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGG-------------------------------------------------
+------------------------------
+>GCF_003691675_PROKKA_00478
+MSGAGYEVFALFQVALLACLAAGGALGALARGRLTDRLGPRGLLTANTTAALVLGATVGL
+AVPELVYASESWGDGQGL--MLVAAVSAVVSGFCLALGTWSTVAAEAADAALARRWGAAA
+RLWTAHLGLGLVAVVVGWGAGLGLHAVLAG
+>GCF_005280335_PROKKA_02182
+MSPALMGASPWEWVLGLAVLAAGGALGALLRLTLQEHLPRRGVLAANTLAAGVLGFSLAL
+ALPSLVYASGLAGDPLGVAGLLVASLTA---GFCLALGTWSTVAGQAADAVLAGRWGAAG
+RIWAAHLGLGLLAAAAGWGLGLGARLLVA-
+>GCF_020097155_PROKKA_02077
+MS-----AGTVLLTVLLAGLAA--AVGAGLRHLADHRWGGRGVLLANVTASALAG-----
+ALFAIGFGPGSA-DPEGPAGAALALGAA--GAFVLALGTWSTVAFQAAQEVLAGRTRRAV
+RVWLVHLASGTAAAVVGV---LAVGFLVR-
+>GCF_023573625_PROKKA_00712
+MSGAGYEVFALLQVALLACLAAGGALGALVRRRLTDRLGPRGLLTANTTAALLLGVTVGL
+AVPELVYASGGGGDGQGL--VLVAAVSAVVSGFCLALGTWSTVAAEAADAVLARRWGTAA
+RLWAAHLGLGLVAVVVGWGAGLGLHAVLAG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000106.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_00762
+MNASFPAGAAAATPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGSPRDVLT
+VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH
+>GCF_003691675_PROKKA_00492
+MNASFPAGAAATPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVRAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMG-GRVVASGPPRDVLT
+VENLDIAYGRGALHGPSTAVEDAADFLDDPAG--GRRH
+>GCF_005280335_PROKKA_02168
+MSRSAAVVPEAAPAPLAVAEHLELRHGDHLAVEASSFTLPAGCVVAVIGPNGSGKSTLLQ
+ALAGVLDPAAGRLEVRG---ESPSRHGRLTSFVMQSLQFPQGVPLTVRDVVTMGRYTTAG
+WFRRLGATDRAAVAAAMERVRVTDLADRHLDQLSGGQRQRVYVAQGLAQEHDVLMLDEPV
+TGLDIVSARTIDEIIHEQPERGVSVVYTTHDLDEAAAADHVVLMD-GRVVASGPPAQVLT
+AANLDAVYGRGALHAPLLV------HLDDPADCSPDRG
+>GCF_020097155_PROKKA_00528
+MN---PAAPAPAIRLADVSAAYDRRRPVFTG---ADLVIDGPGLVRVHGRNGGGKSTLIE
+LVSGYLRPSDGQVRIGGLPAHDPRAHERRRVCRTEPALYPL-----------MDVHDHVV
+FASRWAGADPAEGLARAERYGLGPWMHAPAQTLSTGNRRRLWIVQCTVGAFDTVVLDEPF
+NGLDDESSAVLAAELAAW-ARTRCVVLICHLPPPGLAFDRVVRWPPGQAAADPAP-----
+-----------------------------PAD-PGVRP
+>GCF_020097155_PROKKA_02063
+MTRTVPTAPTPGAGVLAEARGLELRRAAHVAVAPSDLTLPAGVLVAVIGPNGSGKSTLLH
+ALAGTLEPAAGSLTVRG---ESPSRHARRTAFVMQTIPVPQGVPLTVRDVVRMGRYPRVG
+WFGRFGAADREAVDAAMERMSVTDLARRHLDELSGGQRQRVYVAQALAQEHDVLMLDEPL
+TGLDLVSARTIDRLLHEEPARGVSVVHTTHDLDEAAAADFVVLMS-GRVVAAGTPRQVLT
+EANLEAAYGHGVLHGPRLP------FLDDPVD--GVR-
+>GCF_023573625_PROKKA_00726
+MNASFPAGAAAAPPPLAVARALELRHGSHVAVRPSDFTLPARRLIAVIGPNGSGKSTLLT
+ALAGLSDPASGALEVLG---EDPRRRSQRTSFVMQSIGVPQGVPVTVRDVVGMGRYPTLG
+WFRRFRREDRDIVGAAMERMQVADLARRHLDQLSGGQRQRAYVAQGLAQDHDVLLLDEPM
+TGLDIVSARTIDDLLHEEPTRGVSVVYTTHDLDEAAEADHVVLMS-GRVVASGPPRDVLT
+VENLDIAYGRGALHGPSTAVEDAAEFLDDPAG--GIRH
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000109.fa

@@ -0,0 +1,60 @@
+>GCF_002008305_PROKKA_00886
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL
+AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA
+AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL
+TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT-
+--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA
+AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA
+GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA
+ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR---
+-------
+>GCF_003691675_PROKKA_00608
+MTARERPAPSRRPLLRSLALTAQTVREHVTDDPVLLALQVSRRLPPAAVGGAAGILTRLGRNGVVPALGHEMRGERAAAL
+AALGVDEAGR------PVRASRPGAGNVRGLVHRADAALGMGRPDIAETLLGSVPEKRRGAAWTAAAARLAAHRGDLGGA
+AALAARHPRNRHLARRMAGERD----AFRGVAPTVPTEP-----GYRPVPG----RVLHVLTNSLPHTGSGYAQRSHAIL
+TSLRDEGFDAAAVTRPGYPVQIGVPWAAQRDVVDGIRYARLLPARLAQG--QAARIQQHAELLAAHVRRHRPALLHTTT-
+--HFVNALAVEAVARAFGIPWVYEVRGQLADTWAAVRGPEALASERYRLFQER---EAEAARRADGVVTLGAGMRDRLVA
+AGVAEDAVVLCPNAVGPAFVAERVDRDEA-RARLGWDLPTDAFVVGTVSSL-VDYEGLDILLRAAARLAPHRPGLRVHIA
+GDGVARPGLQALAAELGIAELCAFPGRVDREDARLHHAALDVFTVPRRDLPVTRAVTPMKTVEASATGRPVVASDLPALA
+ELVEDERTGLLVPAEDPAALAAALDRLAGDPAERARLGAAGREWALQTRTWEANARRYRTLY-------DRLGVHPR---
+-------
+>GCF_005280335_PROKKA_02050
+MDRPGGLEGAFDRHWRKIRRELGSVYRDYRAGRASTGSALKR----ATRIG----------------LKHGVLAPRDA--
+----LAEFLRLRD--EAVGPTLAGAGPMTMLPGELDSERARIWLSVLERHYPSGPART---AYFEQLRRLALRDGQISTA
+LDATAELASSNTSMARAAVDVNGRMTELSGWLPRLPG-------PVEPVSGCGTNVVLHLLKESRPYLSNGFTSRTQWNL
+LAEKDAGWTPVVLTEPGFPEGMTEGRPSTVEEVDGIEHRRILTGVSYRGVPFDRWLEDFAFLALDHVRNVRPDVLHVSSG
+RRGYETALVGLALREKTGLPLVYEVRSFFEGNWT----PDLDIEEHSEVFRRRREVETRCMIAADRVLTLGEAMRDEIVA
+RGVPAEKVDIVPNGVQLDRF-TPAPRDPAIAARHGITLPT----FGYVSNMDHPREGHELLIRAALLLQERGVEAQCVLV
+GGGRRFDELRALARELGIANRVVFTGPVDHEEVAALYGLIDVFVVPRINERAARYVTPLKPFEAMALRRPVIVSDLPALR
+EIVAAPRRGLTFPVGDVMVLAETIARLLEEPAERQRLGAAGREWVEAERQWVHNGPRYDRAYHAAINARRRAG-------
+-----KG
+>GCF_005280335_PROKKA_02052
+MTSI---LLDFVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL
+GAVGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVNTPGLA--AARARVAWHRGDVEAA
+ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA
+CALRDEGWDVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT-
+--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAV
+AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV
+GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS
+EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAEARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVMAPSA-
+-------
+>GCF_020097155_PROKKA_01946
+MSPR---APRVRRLAANAALTGRTVADHLLDDPVVLALQVSRRLPTGLRAR-------VGG------VLADVPARVAVPR
+G-IGLAMLGREEQLQAALVDADDAPG-PRERARRAEVLLAAGRDEDAERLLADVPADAPGAA--EARARLRWHRGDMTGA
+VLVLSPHGRQGRLRARLAAERD----SLLGRPVCLSAEDRALAADYEPRPG----HVLFVLTNSLPHTGSGYVQRSHSLL
+TAVRDAGWSVAAVTRLGWPVQTGVLAAEDVDRVDGVAYHRLLPAALAPG--FGARLDQHAAALLRLVLRERPAVLHTTT-
+--HWVNAAVTAAVAEAVGIPWVYEVRGQLADTWASTRGPQALMSERYRAFRTR---EAEAAARADGVVTLAETMRARLAE
+DGVDPEDVVLSPNAVGGAFLDAPGERAAA-RRALG--LAPDAEYIGTVSSV-VPYEGLDDLVRVVALLADRRPRLRLLVA
+GDGTALPGLAALAEQLGVRDRVDLLGRVERARAPLCHQALDVFCVPRRDTSVTRDVTPMKPLEAMASARPVLLSRLPALQ
+ELVAEGETGATVPASDPEAWAEAVEALLADPNAAAAMGDRARAWVLAERTWAANARRYTELY-------ARLGAVVDVAD
+RGAVRGG
+>GCF_023573625_PROKKA_00842
+MTSI---LLDSVRALGHAPLVLRTVVDHLRDDPAVLGLQISRRLPLAARVG-------LGR------LAESLPARPGVVL
+GAMGLAAAGRHVDLLEHVEAVLPSAG-APDRVRLADVLTAAQEPDRAQAVLDAVPVDTPGLA--AARARVAWHRGDVEAA
+ISLLGGTGRDGVVRARFASEVR----ALRGGALPLPRADRDRAVGYRPRPG----SALFVLTNSLPHTGSGYAQRSHSLA
+CALRDEGWHVEAVTRLGWPVQTGVLTAARRDMVDGIVYHRLLPSSLARG--FDGRLAQHARMLLDLVLERRPAVLHTTT-
+--HWVNAVVTRAVAEAVGVPWVYEVRGQLADTWASTRGPEALRSDRYALFTAR---EDDAVRSADGVVTLGEQMARRIAA
+AGMDRDAVVLSPNGVGGAFLEEPAPREDA-RRRLG--LSMDDEIVGTVSSV-VPYEGLDDLVRAVAALVDERPRLRLAVV
+GDGVALPALRRLAADLGIEDRLLAPGRVDRSLAPVWHQALDVFCVPRKDTGVTRAVTPMKPLEAMATSRPVLVSDLPALS
+EIVEDGVTGRVLPAEEPEAWAAALAALLDDPAAARGLGARAREWVLGHRTWAANARRYDALY-------RRLGVTAPSA-
+-------

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000112.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_01012
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM
+QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT
+DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD
+>GCF_003691675_PROKKA_00726
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TAAFFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVEV-DGQMLNMGITLQADADLADDQGAAVHAVDGPQTADLGDRPLVWDSAM
+QLAPGVAGAEIVHLVAAPTMEDAYAAVVAEPAHGEVFAFRDSEHSELRAWYIPDEGFVGT
+DTFTVDFHSDHVAHVQTVTVHVGEEISAAYDGFLDAEDGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD
+>GCF_005280335_PROKKA_01876
+M-----------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------THLGDRPLVWDSAM
+QLAPGVEGAEIVHLVAAPTMENTYAEVVTEPAHGEVFAFRDSEHSELRAWYIPEEGFVGT
+---------------------------------------------------DTAAALAAF
+RGDEAAPAPEDEEE----------------------------------------------
+-----
+>GCF_005280335_PROKKA_01877
+MSVIRTRRPSLRHLPAAVAAAGLITTVALAGPAAA-----WDDAHGPQAGSFQAVDHENV
+TTAFFQTYDGYDPEDLTLTITPVAEDGTRLEGGQEVGFTALDVIDGGAVDVLETRRALGA
+AGEGLVRYDVVA-DGQMLNMGITLQADADLADDQGTAVHSVEA-----------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------------RR-
+-----
+>GCF_020097155_PROKKA_01764
+MFV--TRPSCAPRLAAAVLASGL-AAAALAAPASAEQAYDWTDDHGYPHGLFFGMDPESV
+DEATFQTFYGFDPADLTVTVSPSDAEGTPTGPAAAVPFTAVDVLDGGTIDVLETRRVLGE
+AGTGTVAYHVFSGDQKELDMALVVGPDADLADATGGALVAAPGPVRAVLGDMPLSWSADV
+VMAPGVRAMEVRYPVDPALFDDVHPMVMTEAAHGTVVTFRDREDLSVRTWYVPDAGFTGT
+DTFSLDLTSDHVAHLPTVTVHVGQELPAAAAGAPDAQDGVLGGMPLDVEDPAIAAMLQQM
+GALPPAP------EATVPETTVSAEQHTRPGKVQTGGEPIWWLASAAVLGAGALVAARRR
+PGMAG
+>GCF_023573625_PROKKA_00955
+MSVIRTRRPSLRHLPVAVAAAGLVTTVALAGPAAA-----WDDAHGPQAGYFQAVDHENV
+TTALFQTYDGYDPEDLTLTLTPVAEDGTRLEGGQEVEFTALDVIDGGAVDVLETRRALGA
+AGAGLVRYDVVA-DGQMLNMGITLQADTDLADDQGAAVHSVDGPQMAHLGDRPLIWDSAM
+QLAPGVAGAEIVHLVAAPTMESTYAEVVAEPAHGEVFAFRDSGHSELRAWYIPEEGFVGT
+DTFTVDFHSEHVAHVQTVTVHVGEEIPAAYDGFLDAEEGVLNGKPLDLTDPDTAAALAAF
+RADEAAPAPEDEEEQPAPVEDDADEQHTTPDTVETGQSTGWWLAGLGAAAAGVLVAARRR
+LGLTD
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000115.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_01030
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>GCF_003691675_PROKKA_00745
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>GCF_005280335_PROKKA_00186
+MS--EALSRIL--QVWPEIVVALGQTLTMLAVTIPLAVLLGTPLGIWLFTHAPGGLSPSP
+RLHRVVD-AAVSMLRSFPFLILLIAIIPVTRLIVGTTIGTAAVIVPLTVNAIPYFARFVE
+QNLAQLGPGPVEAARAMGATRGQIVRDVLLVDARPALVGSLTIMSVSFISYSAMAGLVGG
+GGIGDFAIRYGYYRYETPLMVVAILLMIGLVALLQFAGTRLSQRLDHRRPRTARRPRRRA
+LAPAG
+>GCF_005280335_PROKKA_01853
+MTWLETLTTNP--AITDALPEALVETLLMVAISGVATVLIGGLLGIVLHVTRPGGLNPMP
+ALYTVLSTVIVNITRSVPYAILMVALIPLTKWLVGTAIGPIAATVSLTIGTAPFFARLVE
+SALREIPSGTVDAAQVMGSTRGQVIRKVLLPEAMPGLIAATTTTLVTLVGYSAMAGLIGG
+GGLGRLAYNYGYQRFQTEVMVVTIVVIVILVQLIQWIGDLLIRRVDHR------------
+-----
+>GCF_020097155_PROKKA_01742
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWAFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FVVNLIRPIPFVILIAALQPLTIAVLGSGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRTVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+>GCF_023573625_PROKKA_00974
+MI--DRFQNLDWGYYGPELMTAVGDTLYMVGWSFILGGILGLLVGLVLYTTRPGGIFANR
+AVYLVTN-FIVNLIRPIPFVILIAALQPLTIAVLGTGIGNTAVVFCMIWASTFGIARIVE
+QNLVSLDPGVIEAARAMGASRMRIVRAVVLPEALGPLILGFTFVIISLVDMSAMAGIIGG
+GGVGNFAIVEGYNRFRPEVTWLAVIVVIVFVQALQLIGNGIARKVMRR------------
+-----
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000116.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_01042
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------MLEPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI
+TRNVADDCSVDSSAWGCTGPIESAPAG
+>GCF_003691675_PROKKA_00755
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------MLKPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFRWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTADIWRTI
+TRNVADDCSVDSSAWGCTGPIESTPAG
+>GCF_005280335_PROKKA_00331
+MP----------------------------------------------------------
+------------------------------------HQLDNADYGSCLNQDESFCPDGE-
+-WVQARTVDITRPDADPLYGRPTCTSDVAAGAGGAR----SFTLEEVRTLLLLDPTIESD
+NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ
+AEFNTPTPTSHVYEETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV
+TRNVAEDCAADPSAWGCTGPIEAPDAP
+>GCF_005280335_PROKKA_00544
+MP----------------------------------------------------------
+------------------------------------HQLDNADYGSCLNQDESFCPDGE-
+-WVQARTVDITRPDADPLYGRPTCTSDAAAGADGAR----SFTLEEVRTLLLLDPTIESD
+NAGRGVRNAETNFYTDAGVETLSTTINGVPVELRATPVSFHWNYGDGTAPRVTHVGGHAQ
+AEFNTPTPTSHVYKETGEYTVTLTTVYIGEYREADGDWVLIPGTITLDAAPVTADIWRTV
+TRNVAEDCAADPSAWGCTGPIEAPDAP
+>GCF_020097155_PROKKA_01735
+MTSRRGDFPACMAVLFALIFLVSAVTLVTPSQAHASSCDTAGRKAQLTDDSLIVGQRCHK
+SSIAEIVGDGLADDQEKSAKATSPTTKVTTLQNACYENLPEPGFENCATQQELICGDQNV
+AWLQPSTKDTARPEDAPVKGDAFCADGSAAPSAPPQPSRPAVSIDDMGEVIAPEPRILAD
+TDGRGVRNAETNFYSPEAVRHETAVIDGVSVEMRLTPVSFIWDYGDGTAPVTTDVGGNPQ
+DGFDVRTPTSHVYDETGTYEVTLTTVYTGEIRYPGQGWEAVPGTIRRTATPVTADIWTTS
+TRNVADDCSADASAWGCAGPVEAPNGG
+>GCF_023573625_PROKKA_00983
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------------------------MSIDEVRTLLVLEPEIRSD
+NGGRGIRNAETNFYADAETRTLVTTLNGVEVELRATPVSFHWDYGDGSPTKTTSVAGQSQ
+PEFNVPTPTSHVYEDTGQYTVRLTTVYIGEYREAGGEWVLIPGTISLDSAPVTANIWRTI
+TRNVADDCSVDSSAWGCTGPIESAPAG
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000117.fa

@@ -0,0 +1,61 @@
+>GCF_002008305_PROKKA_01102
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGP---------------------
+EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGDDPAARRPAATF
+EDFVQPLTTSPGRTVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE
+AAIYGRFGFGAATRWHAVRIDVSGAPAF------TGAPAGGRVTVEEPREIPGLVDELYG
+RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK
+E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV
+SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE
+RLGPAADAVGLD-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL
+VRPSRPLHTLVGF
+>GCF_003691675_PROKKA_00821
+MTPHTDTPEGPSLRRLADAAEARLGEHGLALRDLGVLGP---------------------
+EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGEDPAARRPAATF
+EDFVQPLTTWPGRAVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE
+AAIYGRFGFGAATRWHAVRIDVSGAPAL------TGAPAGGRVTVEEPREMPGLVDELYG
+RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK
+E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV
+SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE
+RLGPAADAVRMG-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL
+VRPSRPLHTLVGF
+>GCF_005280335_PROKKA_01792
+MSIN---PAAAAHAADATAAQDALARHGLVLR---TLAPLSRGFDGADP------AR--A
+EHPAHVRHTAAVEKGFYEEVPQGAAAD-QDLGVSADDAKVLRGVYLSADDPARREPVGTF
+VDWTSRLTTSPGAELPVWMISNVTVSPGHRRRGILRAMMTASLEEAVAAGVPVAALTASE
+STIYGRFGFGAASTARTVRVDVRGDVVLAADAAGRTDEDAGTVLREDPRELAGVVEALHD
+RVRRGTPGSVHRPTGHVIRWEDRSAAKNDGRGSGLFAAVHRDADGAVQGVALYRFDGWGK
+E-----PTTVSVEVFLAATDAAARQLWRYLTRLDLIERLRMTRCPDDGGLEQVLADRRRV
+RTKSVWDDLYLRVLDVPVCLGGRGYAPEVVGEVVLAVADAAGHAAGTWRLRVADG-----
+-VGRAERLADDARADLALDVAHLSAVWLGGVRAG----ALVRAGVVDEREPGAAARLDAL
+LAPAAAVHLLTGF
+>GCF_005280335_PROKKA_01793
+MTPRTDAPDAWLDPAPATA--EALAAHGLEL--LRVPSPWETG--DADPDAPFDHARRWA
+DAPAVRRHTAVLQRNFHEVGDPDFALADRFIGVEQGDRRRLSGVYPQGADPAATDPVGTL
+VDFTKDLNVGDGRMLPAWCLTEVTVSPTHRRRGILRAMMTESLRRAHAARVPIALLTATE
+ATLYRRFGFGVSTYHRSVWLDVTRGVQL------RGRRPDGSFRFVEPTASGALIDGLWR
+RAFEAQAGSVERIRFHAARETDRDPRVGEGRPQGLRAVVYSAPDGEDLGVAVYRVTGSTA
+ELVADDPVTATVVALWAATPEAHRALLEFLGNLDLVVRLRLPAVAADRLLEFLVLDESRI
+YTRGVHHHLWHRVLDVAACFEARPYLHE--GAVTVTVEDDLGYAAGTWEIAAADG-----
+-VGRVRPAPQDA-AELTLDVAELGSVLLGGVKAE----MMREAGILLAHRPGAAADLDTL
+LRQARPPYSLTGF
+>GCF_020097155_PROKKA_01683
+MRPHTDLQ--PTATPRADA--EVLAEQGLAL----VVAP----------------GR--A
+ADPAFERHTTAVERGFYEQVPSGEAMA-QLLEAGEADGRRMVDVLPLGADPATTRPVATF
+EDFRSELTVSPGVAVSAWLISGVTVDPGFRRRGLLRTMMTRSLADAVAAGVPVAALTASE
+AAIYGRFGFGAATRWRRARLDTRGDVRL------RGAPSAGRVTREEPREVGALADELYQ
+HVRRLTPGATQRPTMTAIGWEDRSRFKNDGKGSGLYAAVHRDAAGTAQGIALYRPQGWDV
+E-----PPTVTMELFLALTPDARRGLLTHLTSLDLIERIVWERAPEAGWPEALLEDERRL
+RTERDGDDLYLRILDVPAALGARADLGD--GEVVVDVTDPLGHAAGAWRIRARDG-----
+-VAEVTEAAEGE-AELGLDVADLSAVWLGGHGSAGGVAARVATGLVREVVPGAGARLDAL
+LRPSVPVRSLVGF
+>GCF_023573625_PROKKA_01051
+MTPHTDAPEGPSLRRLADAAEDRLGEHGLALRDLGVLGP---------------------
+EDPAASHFAAAVERGFYETVPTGAALR-QQLEAHAADGRRRLGVYAPGDDPAARRPAATF
+EDFVQPLTTWPGRTVDAWLITDVTVSPDARRRGVLRAMMLRSLADARDAGLCAAALTATE
+AAIYGRFGFGAATRWHAVRIDVSGAPAF------TGAPAGGRVTVEEPREIPGLVDELYG
+RVLPATPGSVQRTSFSVPRWEDREASRNEGRGSGLYAAVHRDDDGRVQGVALYRFEGWEK
+E-----PPTITVTAFLAATADARRGLVHHLARLDLVERIEWGRAPEPGWLEALFVDERRV
+SRHRGSDDLYLRVLNLPAAMAARGWAGD--GEVVVAVEDALGAIDGTWRLTVRQGRGAAE
+RLGPAADAVRMG-AGLRLDAARFSALWLGGHSRGAGAAVLAEAGVVAELRAGAAEAFDGL
+VRPSRPLHTLVGF
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000119.fa

@@ -0,0 +1,90 @@
+>GCF_002008305_PROKKA_01117
+MPKNSSTTVSSAV--EAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA
+EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV
+SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFKDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL
+AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR
+SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE
+RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL
+NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE
+YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW
+IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL
+TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN
+PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY
+KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT
+TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVAAGTPEEVAHVAESHTGRFLAELL
+--------A
+>GCF_003691675_PROKKA_00373
+MVESSSFV-----------------PPKL-SVQPD-VRVLGARENNLQDVDLTVPRDATVVFTGVSGSGKSSLAFGTLYA
+ESQRRYLESVAPYARRLIDQAGVPDVDSITGMPPAVALQQQRGSGNARSTVGSITTLSSLVRMLYSRAG-----------
+------------------------------------------------------------DYP-----------------
+---------------------------------------------------EGQPM--------------------LYAE
+DFSANTVQGACSECHGIGRVYEVNEQQMVPDPSLTIRERAIASWP-----TAWHGHQLRDVLVALGYDVDVPWRDLPKKD
+RDWILYTDETPFVPVHSRLTLSESKAAIEAGVEPSYSGTFVGARRYILDTFANTKSASMKRRVAQFLTAAICPTCNGKRL
+KPEALSVTFEGFDIAEFSQLPLRELATILSGVVAREEDHEAASSDVRPTASRTPEKRAAAVQLASGVLQRLRPLVDLGLG
+YLSLSRTTPTLSGGELQRLRLATQLSSDLFGVVYVLDEPSAGLHPQDVAALLEILDGLKGRGNSLFIVEHSVAVMRHADW
+LVDIGPGAGEHGGRVLYSGPPDGLAGVTESVTRGYLFGGRGLPL----RTPREARSWLRLENVTRNNLHDLTVDIPLGVF
+TAVTGVSGSGKSSLVSQALPSLLGDRLGLAARADDEPVSDESLLADAPEHLEGRVAGPVTGVQRLVVIDQRPIGRTPRSN
+VATYTGLFDHVRRRFADTPEARSRGYKPGRFSFNVAGGRCPTCEGEGSVMVELLFLPSVYTECPDCHGTRYKASTLEVTW
+RGRTIADVLSMSVEEANLFFVGDEEITRSLAALSDVGLEYLRLGQPATELSGGEAQRVKLATELQRAQRGDTLYVLDEPT
+SGLHCADTDRLVAHLQTLVDAGNTVVAAELDMRVVAVADHVIDLGPGAGDAGGTVVAAGTPAHVADQGVGASAGYLAAAL
+QAATNVTPS
+>GCF_003691675_PROKKA_00836
+MPKNSSTTVSSAV--EAHPGGLASGSGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA
+EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV
+SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL
+AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGKKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR
+SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE
+RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL
+NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE
+YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW
+IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL
+TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN
+PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY
+KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT
+TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVATGTPEEVARAAESHTGRFLAELL
+--------A
+>GCF_005280335_PROKKA_01776
+MPKNSSTTVSSAV--ETHAGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA
+EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEVYDYLRLLWARVGVPHCPQCGEPV
+SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFADLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL
+AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEVVAEKGKKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR
+SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLAKEMGFSLDTPWRELEPAQ
+REAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVVPYVLRKHGETESDGARERYESFMREIPCPVCHGARL
+NPTVLNVLVGGLSIAEATRLPLREARDFLAGL------------------ELSARERQIADQVLKEILARLAFLLDVGLE
+YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW
+IVDIGPRAGEHGGEVVHSGSLEDLKANTASITGDYLAGRRAITAPQTRRAPQEGRT-LTVRGARENNLKDVSVDIPLGVL
+TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRAVDGL-----EHLD-----------KVVHVDQSPIGRTPRSN
+PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACSGDGTLKIEMNFLPDVYVPCEVCDGARYNRETLEVTY
+KGKNIAEVLDMPIEEAAQFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRSVYVLDEPT
+TGLHFDDIRKLLQVLQSLVDKGNTVITIEHNLDVVKCADHVIDLGPEGGSGGGTIVATGTPEEVARVEASHTGRFLAELL
+--------A
+>GCF_020097155_PROKKA_01669
+MPKNSSSAAAPARPDAAARGGLASGPARG-SAQHERIVVKGAREHNLKNVDVSIPRDSMVVFTGLSGSGKSSLAFDTIFA
+EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVAHCPVCGEVV
+SKQTPQQIVDQLEQLPERTRFQVLAPVVRGRKGEFVDLFSSLSTQGYARALVDGELIQLSDPPALKKQNKHTIAVVVDRL
+AVKEGIRQRLTDSVETALKLADGLVAVEFVDVDVVAQAGKKNQGDLAGEDAEGNPRFRTFSEKLSCPHGHPQTVDEIEPR
+SFSFNNPFGACPECTGIGSRLQVDPDLVVPNDELSLNEGAILPWSLGKSTSDYWLRVLGGLAKEMKFSLDTPFKDLTAQQ
+RDAVL----------NGKDFKVEVSFRNRFGRERRYTTGFEGVLPYVMRKHGETESDNARERYESFMRQIPCPACHGARL
+NPTVLNVRVGGLSIADATRLPLRESLAFLDGL------------------QLTERELAIADQVVREIRARLEFLLDVGLD
+YLNLERNAGTLSGGEAQRIRLATQIGAGLVGVLYVLDEPSIGLHQRDNRRLIDTLIRLRDLGNTLIVVEHDEDTIAEADW
+IVDIGPRAGEHGGEVVHSGSLDELKANTRSVTGDYLAGRRRIEVPAARRPVDPKRR-LTVKGATENNLKDVTVDIPLGVF
+TAVTGVSGSGKSTLINEILYKVLADKLNGAKMVPGRHRSVAGL-----EHLD-----------KVVHVDQSPIGRTPRSN
+PATYTGVFDQIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY
+KGKNIAEVLDMPIEEAAEFFGAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSTGRTVYVLDEPT
+TGLHFEDIRKLLQVLQTLVDKGNTVLTIEHNLDVVKCADHVIDLGPEGGSGGGTVVATGTPEEVAAVPESHTGRFLAELL
+--------G
+>GCF_023573625_PROKKA_01067
+MPKNSSTTVSSAV--EAHPGGLASGPGGARSGERDRIVVQGAREHNLKDVDVSFPRDAMVVFTGLSGSGKSSLAFDTIFA
+EGQRRYVESLSSYARMFLGRVDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVGTITEIYDYMRLLWARVGVPHCPQCGEPV
+SRQTPQQIVDQLEELPERTRFQVLAPVVRGRKGEFVDLFQDLSTQGFARAVVDGETVQLSDPPVLKKQVKHTIAVVVDRL
+AMKEGIRQRLTDSVETALKLADGLVVAEFVDVEPVAEKGRKNTAEFGGRDAEGNPRYRSFSEKLSCPNGHEQTVDEIEPR
+SFSFNNPFGACPECTGIGSRLQVDPDLVVANDELSLREGAVVPWSLGKSTSDYWLRVLGGLGKEMGFSLDTPWKDLTEAE
+RDAVL----------HGKDFKVEVTFRNRFGRERRYTTGFEGVIPYVMRKHGETESDGARERYESFMREIPCPACHGARL
+NPTVLNVLVGGLSIADATRLPMREAMEFFSGL------------------RLTDRERQIADQVLKEILARLAFLLDVGLE
+YLNLERPAGTLSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLLRLRDLGNTLIVVEHDEDTIAEADW
+IVDIGPRAGEHGGEVVHSGSLADLKANTRSVTGDYLSGRRSIAVPERRRVPEKGRV-LTVRGAQENNLKDVSVEVPLGVL
+TAVTGVSGSGKSTLINEILYKVLANRLNGAKLVPGRHRSVEGL-----EHLD-----------KVVHVDQSPIGRTPRSN
+PATYTGVFDAIRKLFAETPEAKVRGYQQGRFSFNIKGGRCEACAGDGTLKIEMNFLPDVYVPCEVCHGARYNRETLEVTY
+KGKNIAEVLDMPIEEAADFFSAYTRISRYLDTLVDVGLGYVRLGQPATTLSGGEAQRVKLAAELQKRSNGRTIYVLDEPT
+TGLHFDDIRKLLHVLQSLVDKGNTVLTIEHNLDVIKSADHVIDLGPEGGSGGGTIVAAGTPEEVAHVAESHTGRFLAELL
+--------A

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000120.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_01118
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGARVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+>GCF_003691675_PROKKA_00837
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+>GCF_005280335_PROKKA_00163
+MSALAARARAGLAHAVLAVAGARIHASGPDGAEEAEITRERLAALL--------------
+PRQAVFY--ANHTSHLDFVTLWAVLPPALQRRVRPVAAADYW-GSGLRRRVAEGLFHAYL
+VERGKTRRRGPGAASGSGVSPDGGSQLEGMLEILAGGDSLIIFPEGTRGSGEDVARFQRG
+LHALAAAFPQVPVVPVSLVNLGRILPKGEPIPVPHLSTVRFHPPLDPPEPARPPGPGAPA
+SGTAA-TDAPEPGRGEDEAARTAWLERARAVLVQDLSASLRG
+>GCF_005280335_PROKKA_01775
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVTGMDQV
+PAEGPFIMASNHLSFFDSVILQALAP----RPVHFFAKEEYFTGAGVRGRAQRWFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLDSGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALT-TGAPVVPVGLVDTQHLQPPDTNGFRPHRFAVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERLDAYNAAPGAR------------G
+>GCF_020097155_PROKKA_01668
+MAT-------------------------------SEQLRRAVAGAIRLSCRPHVRGLEHV
+PPEGPFIVASNHLSFVDSVILQALCP----RPVGFFAKAEYFEAPGLRGRAQRRFFEAV-
+--GSIPVRRGEQAASVAA--------LEDLVALLDGGHGVGIYPEGTRSRDGRLYRGRTG
+AAWLALT-TGAPVVPVGLRGTERLQPPGTNGFRPHRFTVEMGEPLDFGHPGRRHSLPQRR
+EATATIMAAIAALSGQERVDEYNAAPAAR------------G
+>GCF_023573625_PROKKA_01068
+MAT-------------------------------SEPVRRSAAALLRLTCRPEVVGMEHV
+PARGPFVMASNHLSFVDSVILQALAP----RPVHFFAKEEYFTGTGLRGRVRRRFFESV-
+--GSVPVRRGEQAASVAA--------LESLVGLLESGQGVGIYPEGTRSRDGRLYRGRTG
+AAWLALA-TGAPVVPVGLVGTQHLQPPDTNGFRPHRFSVRVGAPLDFGHPGRRHTLPQRR
+DATAAIMDAIGALSGQERVDAYNAAPGAR------------G
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000121.fa

@@ -0,0 +1,37 @@
+>GCF_002008305_PROKKA_01147
+MADQTTTPTADAQAAGRSVLVTGGNRGIGLAIARAFAANGDRVAITSRSGE-GPEGVL-A
+VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT
+SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR
+SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA
+SDEAAYISGAVIPVDGGLGMGH
+>GCF_003691675_PROKKA_00866
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGE-GPEGVL-A
+VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT
+SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR
+SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA
+SDEAAYISGAVIPVDGGLGMGH
+>GCF_005280335_PROKKA_00771
+MA----------EFDGKVALVTGGGSGIGEACAKDLARGGAKVLVTDINLE-AAERVAEE
+IKADGGEAAAYRLDSASPDDNEKAVAFAEETFGALHLAVNNAGIGAGTEPAGELKIEDWD
+RVIDIDLNGVLYGMRHQLPAMERAGGGAVVNMASIHGTVATGLGASAYTAAKHGVVGLTK
+QAGVDYGPRGVRVNAVGPGYIETPLLAELPDEVHEALVAKHPIGRLGRAEEVAHLVSFLL
+SDKASFLTGAYYLVDGGY-TAP
+>GCF_005280335_PROKKA_01745
+MADQTTPTAADAKASGRSVLVTGGNRGIGLAIARAFAANGDRVAVTSRSGE-GPEGVL-A
+VRADVTDAASV----------DAAFREVEEAHGPVEVLVANAGI-TNDQLLLRMSEEDFT
+SVVDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR
+SITRELGARGVTANVVAPGYIDTEMTQSLGEDLKAQYKKSIPAGRFAQPEEVADVVRWLA
+SDEAAYISGAVIPVDGGLGMGH
+>GCF_020097155_PROKKA_01639
+MAEQT-------EPGGRSVLVTGGNRGIGRAIAEAFLANGDRVAVTSRSGEGGPEGAL-T
+VAADVTDAASV----------DAAFRAVEEAHGPVEVLVANAGV-TNDQLLLRMSEDDFT
+SVVDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLIGMAR
+SITRELGARGITANVVAPGYIDTEMTRSLDEELKAQYRKSIPAGRFAEPEEVADVVRWLA
+SPGAGYVSGAVIPVDGGLGMGH
+>GCF_023573625_PROKKA_01097
+MADQTTTPAADAQAAGRSVLVTGGNRGIGLAIARAFAAHGDRVAITSRSGE-GPEGVL-A
+VRADVTDAASV----------DAAFREVEEVHGPVEVLVANAGI-THDQLLLRMSEDDFT
+SVIDTNLTGAFRVVQRATKGMMRLKRGRIVLVSSVVGLLGSP-GQVNYAASKSGLVGMAR
+SITRELGARGVTANVVAPGYIDTEMTQSLDDELKAQYKTSIPAGRFAAPEEVAGVVRWLA
+SDEAAYISGAVIPVDGGLGMGH
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000124.fa

@@ -0,0 +1,43 @@
+>GCF_002008305_PROKKA_01285
+---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDDVVHAALDAGITFFDV
+ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV
+EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY
+VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA
+PEGSRLSHVRQHMVAD--ADLEQLAGFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA
+GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF
+>GCF_003691675_PROKKA_01004
+---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDAVVHAALDAGITFFDV
+ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV
+EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY
+VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA
+PEGSRLSHVRQHMVAD--ADLEQLAAFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA
+GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF
+>GCF_005280335_PROKKA_01600
+---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTVTLEQDGTDAVVHAALDAGITFFDV
+ADIYGAQPGLSEERLGRA---LGARRDDVVIGTKFGMDMAGANGVDHDARGSRRYIVRAV
+EASLRRLGTDWIDLYQFHTPDPATPIDETLRALDDLVRDGKVRYVGHSNRTGWQIAQAEY
+VARELGTERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGAA
+PEGSRLSHVRQHMVAD--ADLEQLAAFGEF---ARARGITEVQAAIGWLAAQGPVSSVIA
+GATRTGQVAENARAAD--WEATEADLAELDALFPGPEKVALF
+>GCF_020097155_PROKKA_01496
+---MRTVRLGRSGLTVSVVGLGC----NNLGRPGTATMEQEGTDAVVHAALDAGITLFDV
+ADVYGARPGLSEERLGRA---LGSRRDEVVLATKFGMDMGGAAGADGGARGSRRYIVRAV
+EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRSGKVRYIGHSNRTGWQIAQAEH
+AAREIGVERFVSAQNHYNLLDR-RAELEVLPASAEYGLGVLPYFPLANGLLTGKYSDGTA
+PAGSRLSHVRQHMVEE--ADRGQLAAFGAF---ARERGITEVQAAIGWLAAQRPVASVIA
+GATRPGQIAENARAAD--WEATPADLAELDALFPAPPPVALF
+>GCF_020097155_PROKKA_02080
+MSDMIYNRLGSSGLQVSQFSFGSWVTFGNQVDMGLAKDQ-------LAAAKEGGVNFFDN
+AEVYAG--GESESIMGRAIAELGWKRHEYVVSTKLFWGIHGDV-VNMKNTLNRKYLMQGI
+DGSLERLGLDFVDLVFCHRPDPHTPIEETVWAMSDMINRGKALYWGTSEWSADEIRAAWN
+IAERHHLHKPVMEQPQYNLLHRTKVEEEYARLYEDIGLGLTTWSPLASGILSGKYVDG-V
+PEGSRGALKGYDFVKDSIADQETTAKVRQLVDIAAELDVTPAQLALAWTASNPRVSTVIL
+GASSVAQVQENLKALDVIELVTPEVRERLEAVFA--------
+>GCF_023573625_PROKKA_01243
+---MRHTRLGRSGLTVSVVGLGC----NNLGRPGTATLEQAGTDAVVHAALDAGITFFDV
+ADVYGAEPGLSEERLGRA---LGARRDEVVIGTKFGMDMGGVAGDDGGARGSRRYIVRAV
+EDSLRRLGTDWIDLYQFHTPDPATPIEETLRALDDLVRAGKVRYVGHSNRAGWQIAQAEY
+VARELGVERFVSAQNHYNLLDR-RAELEVVPAAAEFGLGVLPYFPLANGLLTGKYSQGDA
+PEGSRLSHVRQHMVAD--ADLEQLAAFGRF---ARERGITEVQAAIGWLAAQGPVSSVIA
+GATRAAQVVENAAAAD--WLATAEDLAELDALFPGPEKVALF
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000125.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_01334
+--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE
+HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL
+GLGRA-------PGTDQRT-------LQALRRDPS-------------------------
+------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK
+GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF
+IAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML
+ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_003691675_PROKKA_01055
+--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE
+HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL
+GLGRA-------PGTDQRT-------LQALRRDPS-------------------------
+------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK
+GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF
+TAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML
+ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_005280335_PROKKA_01557
+--------MTEHTAPTPLPLSLLDLATVRDGASVAEAVAESVEQAQAAERAGFRRVWYAE
+HHNMPAIASSATSVLIAHVAAHTESIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL
+GLGRA-------PGTDQRT-------LQALRRDPS-------------------------
+------------AAER------------FPQDVLELQGYLTGRTRIPG-----IEAYPGK
+GTDVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF
+IAAANVIAADTREEADREWE--AARRARIRMMLGRGRTLSDDEVEMLLHSPAGQQVLTML
+ECTAVGTGEETATWLRDFAAKVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+>GCF_020097155_PROKKA_00131
+---------------MSIPLSVFDPVLLPAETDPREAIDDARTLAAAADALGYRRLWHGE
+HHLNPGVLGSNPALTLALVGPVTQHIRLGSAASLVGPRTPLVLAEDFGLLAAAFPGRIDL
+GLGRAAAPGGPPPGTRAETPTGDGGPAQDPQREPAGAGASSGQDPAAGPSEVDGVVIPAA
+PDLSAALGSPLRAASRALLPTPSTPALDYGAQVDLLLGLLDGTAQHDGAALGQVVARP--
+AVDVEPWVLGSGPGVSAEVAARRGLRFGANYHVSPAGTVAAVRRYRELFRPSPEVPCPVV
+SVSAEVLIADTAAEARRRASGYAAWVLSIRSGAGAVPYPSPAHPEPSRTPQEEALVADRL
+QTRFVGTAEQVAERLDALARLTGADELLISASAHRVEHRVETLTRLAEIWRTA
+>GCF_020097155_PROKKA_01453
+MTADVRPVVPPETAPAGVPLSLLDLATVRGDQRIGEALGQSVELAQTAEAQGFTRVWYAE
+HHNMPGIASSATAVLLAHVAAHTERIRVGSGGVMLPNHSPLVVAEQFGTLAELHPGRVDL
+GLGRA-------PGTDQRT-------LQALRRSPE-------------------------
+------------AADR------------FPQDVLELQGYLRGESRMPG-----IDAYPGR
+GTDVPLWILGSS-AFGANLAAQLGLGYAFASHFAPQMLEHAARLYREHFTPTDALDAPHF
+IAAANVVVADTDEEAQRLWE--ATRRSRVRMFLGRGRHLTEDELDMLMDSPAGEQVLGML
+RHTAVGTPDVVRAWLDDFAARVEADELIVTAAAVDHPARVRTLELLGEHVIRR
+>GCF_023573625_PROKKA_01290
+--------MTEHTAPTPLPLSLLDLALVRDGAPMGEAFAESVEQARVAEAAGFRRVWYAE
+HHNMPSIASSATAVLIAHVAAHTDSIRLGSGGVMLPNHSPLVIAEQFGTLAELHPGRIDL
+GLGRA-------PGTDQRT-------LQALRRDPS-------------------------
+------------AAER------------FPQDVLELQGYLTGQSLIPG-----IDAYPGK
+GTNVPLYILGSS-AFGAQLAAQLGLGYAFASHFAPQMLEHAARLYREHFEPSEALAEPHF
+IAAANVIAADTEEVAEREWQ--AAQRARIRMMLGRGRTLTDDEVEMLLHSPAGQQVLGML
+ECTAVGTGPTTAAWLHDFAARVQADELIITTAAQDAGVRRRTLELLGEHVVRA
+ 

Biomni/experiments/bioagent_bench/runs/scale_3000/comparative-genomics_20260520_141735/orthofinder_results/Results_May20/MultipleSequenceAlignments/OG0000126.fa

@@ -0,0 +1,49 @@
+>GCF_002008305_PROKKA_01341
+MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ
+TAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI
+DHSWIGTDLRGTFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV
+-----HVITLGTGIGGAMIHDGMLVP-----NFEVGSLELD-------------------
+-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG
+GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG--
+N
+>GCF_003691675_PROKKA_01061
+MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ
+PAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI
+DHSWIGTDLRGRFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV
+-----HVITLGTGIGGAMIHDGVLVP-----NFEVGSLELD-------------------
+-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG
+GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG--
+N
+>GCF_005280335_PROKKA_01551
+MT-THTTTAQRS----SKHP-TTIGIDVGGTGMKGGLVRLGSGPKSGTLRGDRFRIPTPQ
+PAMAEPVAATLAAITAELDARDKAPAPTAPLGVCFPSIV----------KDGVCLSANNI
+DPSWIGTDLKAAFEEHLRRPV-------------RVVNDADAAGLAEARYGAGRGVSGLV
+-----LVITLGTGIGGAMVHDGVLVP-----NFEVGSLELD-------------------
+-------------GVMAETRASAKARERED-LSWAEYAQRLQRFFSHVEHVFSPDLFIVG
+GGISKRPDDYLPLLSL------------RTP-IVPAQLRNNAGIVGAALAAHDSLADA--
+R
+>GCF_020097155_PROKKA_01415
+MH--RSRPAPPSPPAPSAYPRRLLGVDLGGTAAKAGVLELARDGRARILARSRAAHAGAD
+PASAVTRA---------------AADALSRAGVRVPDGAGFACAAWLDPATGRARASPHL
+-PSLVGIR-----PAALLTPVLEAAGAAGHGLVPVALNDADAAALAESRLGAARPAPGDL
+PGAPTLFVALGTGVGGAVIVDGAVLPGARGMHGEAGHICVDPDGPACPCGARGCWELYAS
+ASALARTLPGRPIADVLEAAVAGPGPERDAVLDAGEW---LGRGLAPAVCLLDPVRVVVG
+GGLMAAGELLLPTARAALRRALPTAAADRPPELVAAALGNDAGWIGAALADGARV-----
+-
+>GCF_020097155_PROKKA_01447
+MSFPNTGVIPRLPPAPSKHP-SVLGVDIGGTGMKGGIVRLGHGPKSGTLRGDRFRLDTPQ
+PASPATMARTLAQIVSELDHREKAPDADSRVGVCFPSIV----------QHGVCRSANNI
+DPSWIGVSLQDTFEEALQRPV-------------TVVNDADAAGLAEARYGAGAGVPGLV
+-----MVITLGTGIGGAMINDGVLVP-----NFEVGSLELD-------------------
+-------------GVMAESRASAKAREREG-LDWPEYALRLQRFFSHLERIFSPDLFIVG
+GGISKRPHDYLPLLQL------------ETP-IVPAMLQNNAGIVGAALAAHADPADGLL
+R
+>GCF_023573625_PROKKA_01296
+MT-THTSTAQRS----SKYP-TTIGIDVGGTGMKGGLVRLGSGPKAGTLRGDRFRIPTPQ
+PAMPEPVAATLAAITAELDGREKAPKPSAPLGVCFPSIV----------KDGVCLSANNI
+DHSWIGTDLRGRFEEHLRRPV-------------TVVNDADAAGLAEARYGAGRGVRGLV
+-----HVITLGTGIGGAMIHDGVLVP-----NFEVGSLELD-------------------
+-------------GVMAESRASAKARERDQ-LSWAEYAERLQRFFSHVERIFSPDLFIVG
+GGISKRPDDYLPLLRL------------RTP-IVPAQLQNNAGIVGAALAAHGSLADG--
+N
+