#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on July 09, 2025; 13:35 GMT TreeBASE (cc) 1994-2008 Study reference: Nozaki H., Maruyama S., Matsuzaki M., Nakada T., Kato S., & Misawa K. 2009. Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes. Molecular Phylogenetics and Evolution, 53(3): 872-880. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10068] BEGIN TAXA; TITLE M4557; DIMENSIONS NTAX=32; TAXLABELS Arabidopsis_thaliana Aureococcus_anophagefferens Candidatus_Protochlamydia_amoebophila Chlamydia_muridarum 'Chlamydia trachomatis 434-Bu' 'Chlamydia trachomatis D-UW-3-CX' Chlamydomonas_reinhardtii Chlamydophila_abortus Chlamydophila_caviae Chlamydophila_felis Chlamydophila_pneumoniae Chlorella_sp._NC64A Eimeria_sp. Emiliania_huxleyi Mesostigma_sp. Micromonas_pusilla_CCMP_1545 Micromonas_sp._RCC299 Oryza_sativa Ostreococcus_lucimarinus_lucimarinus Ostreococcus_lucimarinus_sp._RCC809 Ostreococcus_lucimarinus_tauri Phaeodactylum_tricornutum Physcomitrella_patens_sp._1 Physcomitrella_patens_sp._2 Polytomella_parva Populus_trichocarpa Selaginella_sp._1 Selaginella_sp._2 Thalassiosira_pseudonana Toxoplasma_gondii Volvox_sp. Zea_mays ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M4561] TITLE fabl_291x32; LINK TAXA = M4557; DIMENSIONS NCHAR=291; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana IDLRGKRAFIAGIADDNGYGWAIAKSLAAAGAEILVGTWVPALNIFETSLRRGKFDQSRVLPDGSLMEIKKVYALDAVFDNPEDVPEDVKTNKRYAGSSNWTVQEAAECVKKDFGSIDILVHSLANGPEVSKPLLETSRKGYLAAISASSYSFVSLLRHFLPIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAYEAGRKSNIRVNTISAGPLGSRAAKAIGFIDTMIEYSYNNGPIQKTLTADEVGNAAAFLASPLASAITGATIYVDNGLNAMGVALDS Aureococcus_anophagefferens GDLTGKVAFVAGVADSTGYGWAIAKALAEAGATIIVGTWPPVLNIFKSSLDKGKLDDDRKLSNGGMMDIAKVYPLDAVFDTPDDVPDDIKANKRYAGLESFTISEVAESIAKDYGKIDILVHSLANGPEVTKPLLETSRKGYLAANSASAYSFVSLVQHVAPIMHEGGAAVSLTYIASEDVIPGYGGGMSSAKAALESDTRTLAWEAGRKYGVRVNTISAGPLKSRAASAISFIDLAIDYSKVNSPLNKDLYADDVGASAFFLLSDLSRAVTGVTLYVDNGLHSMGMAVDS Candidatus_Protochlamydia_amoebophila INLKGKKAFIAGVGDDQGFGWAIAKALAEAGAEIIIGTWTPILKIFTSSLQAGKFDASRRLPNGSLLTFAKIYPLDASFDKPEDVPEEIRENKRYKGVGGYTISEVCEAIGKDFGKIDIFVHSLANAPEVQKPLLETSRKGYLAALSSSSYSFVSLLSHLGPYLNSQGSALTLTYLASEKIIPGYGGGMSSAKAALESDTRTLAWEAGRKWNIRVNTISAGPLRSRAARAIGFIDRMINYSQVNAPLQEELKACEVANVAAFLGSDLACAITGSTIYVDYGLHAMGVGMDS Chlamydia_muridarum IDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSWELGKLNESRKLSNGELLTLAKIYPMDASFDTPEDVPQDILENKRYKDLSGYTVSEVVEQVKKDFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNEGASTISLTYLASMRAVPGYGGGMSAAKAALESDTKVLAWEAGRRWGIRVNTISAGPLASRAGKAIGFIERMVDYYLDWAPLPSPMEAEQVGAAAAFLVSPLANAITGETLYVDHGANIMGIGPEM 'Chlamydia trachomatis 434-Bu' IDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSWELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKDFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEM 'Chlamydia trachomatis D-UW-3-CX' IDLTGKIAFIAGIGDDNGYGWGIAKMLAEAGATILVGTWVPIYKIFSQSLELGKFNASRELSNGELLTFAKIYPMDASFDTPEDIPQEILENKRYKDLSGYTVSEVVEQVKKHFGHIDILVHSLANSPEIAKPLLDTSRKGYLAALSTSSYSFISLLSHFGPIMNAGASTISLTYLASMRAVPGYGGGMNAAKAALESDTKVLAWEAGRRWGVRVNTISAGPLASRAGKAIGFIERMVDYYQDWAPLPSPMEAEQVGAAAAFLVSPLASAITGETLYVDHGANVMGIGPEM Chlamydomonas_reinhardtii VDLRGKKAFIAGVADDQGFGWAIAKALAEAGAEISLGVWVPALNIFKTSLDKGKFDESRKLSDGSLMTFSHIYPMDAVFDTMADVPEEVATNKRYAGNKAWTVSEVAESVKKDSGNIDILVHSLANGPEVVKPLLEVSRKGYLAALSASSYSLISMVQRFGPLMNEGGAVISLTYNASNRIIPGYGGGMSSAKAALESDTRVLAYEAGRKYKVRVNTISAGPLGSRAAKAIGFIDDMIRYSYENSPIQKELAAIEVGNVDAFLCSPLSSAVTGHVMFVDNGLNVMGLAEDS Chlamydophila_abortus IDLTGKIAFIAGIGDDQGYGWGIAKALAEAGATILVGTWVPIYKIFTQSWDLGKFDQSRKLSDGNLLEIKKIYPMDASFDKPEDVPEDIAENKRYKGISGYTVSEVVERITKDFGHIDILVHSLANSPEISKPLLETSRKGYLAALSTSSYSLVSLLAHFGPIMPQGSTSVSLTYLASSRAVPGYGGGMSAAKAALESDTKMLAWEAGRKWGVRVNTISAGPLASRAGKAIGFIEQMVDYYLDWTPIPEPMTTEQVGAVAAFLASPLASAITGETLYVDHGANIMGIGPEM Chlamydophila_caviae IDLTGKVAFIAGIGDDQGYGWGIAKVLAEAGATIIVGTWVPIYKIFSQSWDLGKFDESRKLSDGSLLEIKKVYPMDASFDKPEDVPQDITENKRYKGISGYTISEVVEQVTKDFGHIDILIHSLANSPEISKPLLETSRKGYLAALSTSSYSLVSLLAHFGPIMHPGGSSISLTYLASSRAVPGYGGGMSAAKAALESDTKMLAWEAGRKWGIRVNTISAGPLASRAGKAIGFIEQMVDYYLDWTPIPNPMTTEQVGAAAAFLVSPLASAITGETLYVDHGANIMGIGPEM Chlamydophila_felis IDLTGKVAFIAGIGDDQGYGWGIAKVLAEAGATIIVGTWVPIYKIFSQSWDLGKFDESRKLSDGSLLEIKKVYPMDASFDKPEDVPSDIAENKRYKGISGYTISEVVEQVTKDFGHIDILIHSLANSPEISKSLLETSRKGYLSALSTSSYSLVSLLAHFGPIMNPGGSSISLTYLAASRAVPGYGGGMSAAKAALESDTKMLAWEAGRKWGIRVNTISAGPLASRAGKAIGFIEKMVDYYLDWSPIPEPMTTEQVGAAAAFLVSSLASAITGETLYVDHGANIMGIGPEM Chlamydophila_pneumoniae IDLTGKVAFVAGIGDDQGYGWGIAKLLAEAGATIIVGTWVPIYKIFSQSWELGKFNESRKLSNGTLLEIAKIYPMDASFDSPEDVPEDIAENKRYKGITGFTISEVAEQVKKDFGHIDILVHSLANSPEISKSLLETSRKGYLAALSASSYSFVSLLSHFGSIMNRGGSTISLTYLASMRAVPGYGGGMSSAKAALESDTKTLAWEAGRRWGIRVNTISAGPLASRAGKAIGFIERMVDYYQEWAPIPEAMNAEQVGAVAAFLASPLASAITGETLYVDHGANVMGIGPEM Chlorella_sp._NC64A IDLRGKKAFIAGVADDQGFGWAIAKCLAEAGAEISLGVWVPALNIFETSFRRGKFDESRRLSNGSLMEFAHIYPMDAVFDTMDDVPADVKDNKRYAGNEGWTVSECAAKVAKDWGKIDILVHSLANGPEVQKPLLETSRRGYLAAMSASSYSFVSLLQRFGPLMNEGGAVISLTYVAADRVIPGYGGGMSSAKAALESDTKVLAYEAGRKYSVRVNTISAGPLGSRAAKAIGFIDDMIRYSYENAPIQKELAATEVGAVATFLCSPLASAVTGQTVYVDNGLSIMGLAGDS Eimeria_sp. VDLRGKTAFVAGVADSNGYGWAICKLLRAAGARVLVGTWPPVYSIFKKGLESSRFEQYAQEPSSVDLVFDKIYPLDAVFDTPQDVPPEVSSNKRYAGVGGFTISEVAEAVRADVGQIDILVHSLANGPEVTKPLLQTSRKGYLAAVSSSSYSFVSLLQHFLPLMKEGGSALALSYIASEKVIPGYGGGMSSAKAALESDCRTLAFEAGRARAVRVNCISAGPLKSRAASAIGFIDLAIDYSEANAPLQKELESDDVGRAALFLLSPLARAVTGATLYVDNGLHAMGQALDS Emiliania_huxleyi VDLTGKTAFVAGVADSTGYGWAICKALANAGCKITVGTWPPVLGIFQKSLASGKFDEDMILDDGSKMVIEKIYPLDAVFDTKADVPEDVLSNKRYAGLDGFSIEETAEAVKADYGKIDILVHSLANGPEVQKPLLETSRAGYLAAASASSYSLVSLVSKFGPIMNEGGSVLSLTYIASEKVIPGYGGGMSSAKAALESDTRVLAWEAGRKYNIAVNTISAGPLKSRAASAISFIEVGIDYCKANAPLAKDLYSDDVGQTACCLLSPLFGAVTGVTLYVDNGMHAMGMIQDK Mesostigma_sp. IDLTGKKCFIAGVADDQGFGWAIAKAMAEAGATIILGTWVPALNIFETSFRKGKFDDNRKLADGSMLDFAKIYPMDAVFDTPEDVPEEVKTNKRYAGAGAFTVQEVADAVKKDFGNIDIIVHSLANGPEVAKPLLETSRKGYLSANSASSYSFVSMVQRFGPIMNPGGAAIALTYLAGERVVPGYGGGMSSAKASLDSDVKVLAYEAGRKWNIRVNAVSAGPLASRAAKAIGFIDVMIRYSAANAPLMKNLYAEDVGATATFLCSPLAKSITGEILHCDNGLNTMGVAADS Micromonas_pusilla_CCMP_1545 IDLRGKKAFVAGVADDQGFGWAISKCLQEAGAEVILGTWVPALNIFETSLRRGKFDESRKLSDGSLMEFAKVYPMDAVYDTMDDVPEDVLANKRYAGNEKWTVSECAAEVEKDFGKIDILVHSLANGPEVMKPLLETSRNGYLAAMSASSYSNVSMLQRFGPLMNPGGACISLTYLASERIIPGYGGGMSSAKAALESDTQVLAYEAGRKWGIRVNTISAGPLGSRAAKAIGFIDDMINYSMSNAPLNKPLTAMEIGQTAAFLCSPLASGITGSTVYVDNGLNAMGLAGDS Micromonas_sp._RCC299 IDLRGKKAFVAGVADDQGFGWAISKCLAQAGCEVILGTWVPALNIFETSLRRGKFDESRKLSDGSLMEFAKVYPMDAVFDTYDDVPEEIRTNKRYAGNEKWTVAECAEQVEKDFGKIDILVHSLANGPEVAKPLLETSRNGYLAALSASSYSKVSMLQRFGPIMNKGGAAISLTYLASEKIIPGYGGGMSSAKAALESDTQVLAYEAGRKWGIRVNTISAGPLGSRAAKAIGFIDDMINYSLTNAPLAKPLTAMEIGQTAAFLCSPLASGITGSCIYVDNGLHAMGLATDA Oryza_sativa IDLRGKRAFIAGVADDNGYGWAIAKALAAAGAEILVGTWVPALNIFETSLRRGKFDESRKLPDGSLMEIVKVYPLDAVYDSPEDVPEDVKGNKRYAGSSNWTVKEVAESVKNDFGSIDILVHSLANGPEVTKPLLETSRRGYLAALSASSYSFVSLLQHFLPIMNPGGASISLTYIASERAIPGYGGGMSSAKAALESDTKVLAFEAGRKGKIRVNTISAGPLGSRAAKAIGFIEKMIEYSYVNAPLQKELLADEVGNTAAFLVSPLASAITGSTVYVDNGLNTMGLAVDS Ostreococcus_lucimarinus_lucimarinus VDLRGKKAFVAGVADDNGFGWAISKALSEAGAEVILGTWVPALNIFETSYRRGKFDESRKLSDGSMMTFSKIYPMDAVFDAMDDVPEDIATNKRYAGNEKWTVSEVAKCVEEDFGKIDVLVHSLANGPEVAKPLLETSRKGYLAAISASSYSNVSMIQHFGPLMNKGGAAISLTYLASEQIIPGYGGGMSSAKAALESDTRVLAYEAGRKWGIRVNTISAGPLGSRAAKAIGFIDKMINYSLSNAPLKKPLEAIEIGNTAAFLCSPLASGITGATIYVDNGLNAMGLAETA Ostreococcus_lucimarinus_sp._RCC809 VDLTGKKAFVAGVADDNGFGWAISKALSEAGAEVILGTWVPALNIFETSYKRGKFDESRKLSDGSMMTFSKIYPMDAVFDDMDDVPEDIKTNKRYAGNEKWTVSEVAKCVEEDFGKIDILVHSLANGPEVAKPLLETSRKGYLAAISASSYSNVSMIQHFGPLMNKGGAAISLTYLASEKIIPGYGGGMSSAKAALESDTRVLAFEAGRKWGIRVNTISAGPLGSRAAKAIGFIDKMINYSFANAPLNKPLEAIEIGNTAAFLCSPLASGITGATIYVDNGLNNIGLAQDA Ostreococcus_lucimarinus_tauri VDLRGKKAFVAGVADDNGFGWAISKALSEAGAEVILGTWVPALNIFETSYRRGKFDESRKLSDGSLMEFAKIYPMDAVFDTPDDVPEDIATNKRYAGNEKWTVSEVAKCVEADFGKIDIVVHSLANGPEVAKPLLETSRKGYLAAVSASSYSMVSMVQHFAPLMNEGGAVISLTYIASEAVIPGYGGGMSSAKAALESDTRVLAYEAGRKHGIRVNTISAGPLGSRAAKAIGFIDKMINYSLSNAPLAKPLGAIEIGNTAAFLCSPLASAITGQTIYVDNGLSVMGSATSA Phaeodactylum_tricornutum VDLKGKVAFVAGVADSTGYGWAIAKALAEAGATIIVGTWPPVLKIFQMGLKKGQFNEDSTLADGSLMTIEKVYPLDAVFDAPDDVPDEIKENKRYAGLDGYTISEVAKAVEADYGKIDILVHSLANGPEVTKPLLETTRKGYLAASSASAYSAVSLLQKFGPIMNEGGAMLSLTYIASEKVIPGYGGGMSSAKAQLESDTRTLAYEAGRKWGIRVNTISAGPLKSRAASAIGFIEYAIDYSKANAPLEQDLYSDDVGNASLFLTSPMARTVTGVTLYVDNGLHSMGMALDS Physcomitrella_patens_sp._1 IDLRGKRAFIAGVADDQGFGWAIAKALSAAGAEILVGTWVPALNIFESSLRRGKFDESRRLPNGGLLEIAKVYPLDAVFDTPDDVPEDIKNNKRYAGSEAWTVKECAEAVKADFGTIDILVHSLANGPEVTKPLLETSRNGYLAAVSASTYSYISLLKYFAPIMNPGGSSLSLTYVASEQIIPGYGGGMSSAKAALESDTRVLAFEVGRKYGIRVNTISAGPLRSRAAKAIGFIDDMINYSCANAPLQKELDADDVGNAAAFLASPLASSVTGTLLYVDNGLHAMGLAVDS Physcomitrella_patens_sp._2 IDLRGKRAFIAGVADDQGFGWAIAKALAAAGAEILVGTWVPALNIFETSLRRGKFDESRQLPTGGLLEIAKVYPLDAVFDTPEDVPEDIKNNKRYAGSTAWTVQECAEAVKADFGSIDILVHSLANGPEVTKPLMETSRKGYLAAVSASTYSYVSLLKYFAPIMNPGGSALSLTYLASEKIIPGYGGGMSSAKAALESDTRVLAFEAGRKYGIRVNTISAGPLKSRAAKAIGFIDDMINYSSANAPLQKELEADDVGHAAAFLSSPLASAVTGTLLYVDNGLHAMGLAVDS Polytomella_parva IDLRGKKAFIAGVADDQGFGWAIAKCLAEAGCEISLGVWVPALNIFESSLRRGKFDANRKLSNGKLMEFSKIYPMDAVFDTLADVPKDILSNKRYAGNSKWTVAEVAESVKADSGNIDILVHSLANGPEVIKPLLETSRKGYLAALSASSYSLISLVQRFGPLMNKGGSVISLTYNASNRIIPGYGGGMSSAKAALESDTRVLAYEAGRKYGVRVNTISAGPLGSRAAKAIGFIDDMIRYSEENSPIQKGLSAEEVGAVATFLLSPLASGVTGHVMFVDNGLNAMGLATDA Populus_trichocarpa VDLRGKRAFIAGVADDNGYGWAIAKSLAAAGAEIIVGTWVPALNIFESSLRRGKFDESRVLPDGSLMEITKVYPMDAVYDSLDDVPEDVKSNKRYAGSSKWTVKELVESVKQDFGSIDILVHSLANGPEVSKPLLETSRNGYLAAISASSYSFVSLLKEFVSIMNPGGASISLTYIASERIIPGYGGGMSSAKAALESDTRVLAFEAGRKHKIRVNTISAGPLRSRAAKAIGFIDMMIDYSSANAPLQKELSAEEVGNAAAFLASPLASAITGAVVYVDNGLNAMGVGVDS Selaginella_sp._1 IDLTGKRAFIAGVADDQGYGWAIAKTLASAGAEILVGTWVPALNIFETSLRRGKFDESRQLPNGSLFEISKVYPLDAVFDCPEDVPEDIKNNKRYAGASAWTVTEVVDSVKKDFGSIDILVHSLANGPEVSKPLLETSRKGYLAASSASAYSHVSLLRHFAPIMNQGGSVISLTYMASEKTIPGYGGGMSSAKAALESDTRVLAFEAGRKYKIRVNTISAGPLKSRAAKAIGFIEKMIDYSKANSPLQRDLEADDIGNAATFLASPLASAISGTVFYVDNGLHTMGMALDS Selaginella_sp._2 IDLTGKRAFIAGVADDQGYGWAIAKTLASAGAEILLGTWVPALNIFETSLRRGKFDESRQLPNGSLFEISKVYPLDAVFDCPEDVPDEIKNNKRYAGASAWTVTEVVDSVKKDFGSIDILVHSLANGPEVSKPLLETSRKGYLAASSASAYSHVSLLRHFAPIMNQGGSVISLTYMASEKTIPGYGGGMSSAKAALESDTRVLAFEAGRKYKIRVNTISAGPLKSRAAKAIGFIEKMIDYSKANSPLQRDLEADDIGNAATFLASPLASAISGTVFYVDNGLHTMGMALDS Thalassiosira_pseudonana VDLTGKVAFVAGVADSSGYGWAIARALASAGATIIVGTWPPVLKIFEMGIRKGSFDDDSILPDGSKMEIAKVYPLDAVFDTAEDVPEEIKTNKRYAGLDGYTIEEVAKAVEADYGKIDILVHSLANGPEVTKPLLETSRKGYLAASSASAYSAVSLLQKFGPIMNEGGNMLSLTYIASEKVIPGYGGGMSSAKAQLESDTRTLAFEAGRKWNVRVNTVSAGPLKSRAASAIGFIEYAIDYSKANAPLAQDLYNDDVGNSALFLCSGLARTVTGVTLYVDNGLHAMGMALDS Toxoplasma_gondii IDLRGQTAFVAGVADSHGYGWAIAKHLASAGARVALGTWPPVLGLFQKSLQSGRLDEDRKLPDGSLIEFAGVYPLDAAFDKPEDVPQDIKDNKRYAGVDGYTIKEVAVKVKQDLGNIDILVHSLANGPEVTKPLLETSRKGYLAASSNSAYSFVSLLQHFGPIMNEGGSAVTLSYLAAERVVPGYGGGMSSAKAALESDTRTLAWEAGQKYGVRVNAISAGPLKSRAASAIGFIDYAIDYSYNNAPLRRDLHSDDVGGAALFLLSPLARAVSGVTLYVDNGLHAMGQAVDS Volvox_sp. VDLRGKKAFIAGVADDQGFGWAIAKALAEAGAEISLGVWVPALNIFKTSLEKGKFDASRKLSDGSLMTFSHIYPMDAVFDTMADVPEEVATNKRYAGNKNWTVSEVAESVKQDSGKIDIVVHSLANGPEVVKPLLETSRKGYLAALSASSYSLISMVQRFGPIMKEGGAVISLTYNASNRIIPGYGGGMSSAKAALESDTRVLAYEAGRKFKVRVNTISAGPLGSRAARAIGFIDDMIRYSYENSPIQKELAAIEVGNVAAFLVSPLSSAVTGHVMFVDNGLNVMGIATDS Zea_mays IDLRGKRAFIAGVADDNGYGWAIAKALAAAGAEILVGTWVPALNIFETSLRRGKFDESRKLPDGSLMDIVKVYPLDAVYDSPDDVPEDVKSNKRYAGASNWTVKEVVESVRNDFGSIDILVHSLANGPEVTKPLLETSRRGYLAAISASSYSYVSLLQHFLPIMNPGGASISLTYIASERAIPGYGGGMSSAKAALESDTRVLAFEAGRKGKIRVNTISAGPLGSRAAKAIGFIEKMIEYSYVNAPLQKELLADEVGNTAAFLVSSLASAITGSTVYVDNGLNTMGLAIDS ; END;