#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 September 19, 2025; 10:57 GMT TreeBASE (cc) 1994-2008 Study reference: Aguilera F., Mcdougall C., & Degnan B.M. 2013. Origin, evolution and classification of type-3 copper proteins: Lineage-specific gene expansions and losses across the Metazoa. BMC Evolutionary Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13985] [ The following blocks are input data for analysis step 11029 ] BEGIN TAXA; TITLE TaxaForAnalysisStep11029; DIMENSIONS NTAX=96; TAXLABELS Agaricus_bisporus_tyr Aplysia_californica_Hc Aspergillus_aculeatus_tyr Bacillus_megaterium_tyr1 Bacillus_megaterium_tyr2 Brugia_malayi_TYR1 Brugia_malayi_TYR2 Brugia_malayi_TYR3 Brugia_malayi_TYR4 Caenorhabditis_briggsae_TYR1 Caenorhabditis_briggsae_TYR2 Caenorhabditis_briggsae_TYR3 Caenorhabditis_briggsae_TYR4 Caenorhabditis_briggsae_TYR5 Caenorhabditis_briggsae_TYR6 Caenorhabditis_elegans_TYR1 Caenorhabditis_elegans_TYR2 Caenorhabditis_elegans_TYR3 Caenorhabditis_elegans_TYR5 Caenorhabditis_elgans_TYR4 Caenorhabditis_remanei_TYR1 Caenorhabditis_remanei_TYR2 Caenorhabditis_remanei_TYR3 Caenorhabditis_remanei_TYR4 Caenorhabditis_remanei_TYR5 Candidatus_nitrosopumilus_tyr Ciona_intestinalis_HcB Ciona_intestinalis_HcC Ciona_intestinalis_HcD Ciona_intestinalis_HcE Ciona_intestinalis_HcF Ciona_intestinalis_HcG Ciona_intestinalis_HcH Ciona_intestinalis_HcI Dictyostelium_discoideum_tyr1 Dictyostelium_discoideum_tyr2 Ectocarpus_siliculosus_tyr1 Ectocarpus_siliculosus_tyr10 Ectocarpus_siliculosus_tyr11 Ectocarpus_siliculosus_tyr12 Ectocarpus_siliculosus_tyr13 Ectocarpus_siliculosus_tyr14 Ectocarpus_siliculosus_tyr15 Ectocarpus_siliculosus_tyr18 Ectocarpus_siliculosus_tyr2 Ectocarpus_siliculosus_tyr3 Ectocarpus_siliculosus_tyr4 Ectocarpus_siliculosus_tyr5 Ectocarpus_siliculosus_tyr6 Ectocarpus_siliculosus_tyr7 Ectocarpus_siliculosus_tyr8 Ectocarpus_siliculosus_tyr9 'Ectocarpus_siliculosus tyr16' 'Ectocarpus_siliculosus tyr17' Glycine_max_CO1 Glycine_max_CO10 Glycine_max_CO11 Glycine_max_CO12 Glycine_max_CO2 Glycine_max_CO3 Glycine_max_CO4 Glycine_max_CO5 Glycine_max_CO6 Glycine_max_CO7 Glycine_max_CO8 Glycine_max_CO9 Hydra_magnipapillata_tyr Illex_argentinus_tyr1 Illex_argentinus_tyr2 Lottia_gigantea_Hc Lottia_gigantea_tyr1 Lottia_gigantea_tyr2 Megathura_crenulata_Hc Nematostella_vectensis_tyr1 Nematostella_vectensis_tyr2 Nematostella_vectensis_tyr3 Nematostella_vectensis_tyr4 Neurospora_crassa_tyr1 Neurospora_crassa_tyr2 Neurospora_crassa_tyr3 Neurospora_tetrasperma_tyr1 Neurospora_tetrasperma_tyr2 Neurospora_tetrasperma_tyr3 Nitrosomonas_europeae_tyr Nucula_nucleus_Hc Oryza_sativa_CO Pinctada_fucata_tyr1 Pinctada_fucata_tyr2 Pinctada_fucata_tyr3 Pinctada_fucata_tyr4 Polysphondylium_pallidum_tyr1 Sepia_officinalis_Hc Sepia_officinalis_tyr Streptomyces_tsukubaensis_tyr Streptomyces_venezuelae_tyr Vitis_vinifera_CO ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M16277] TITLE alignment_alpha; LINK TAXA = TaxaForAnalysisStep11029; DIMENSIONS NCHAR=114; 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 ] [ . . . . . . . . . . . ] Agaricus_bisporus_tyr MRKEYRMMSEAERARWHNALNTLKRNGEYDRLSRQHLEVGAHSGPGFLPWHREYLKRFEIALRDLVFIPYWDSVVVTGPFEYSHSNIHLWIGGDMKPSTSANEPIFFMHHSFVD Aplysia_californica_Hc MRRPAQWVDDDYLNKYKEAVRLMRDPRNFMQQAKIHCAYCVHGNWLFAPFHRWYLYFHERILGITFALPFWNWDIVDLANEGPHNNVHRWTGIDMGYAWAARDPIFFAHHSNVD Aspergillus_aculeatus_tyr MRKPAHMVDEEYIAKLEKGIALMKDPRNFIQQAKVHCAYCIHRSWFFFPFHRWYIYFFERILGLNFALPFWNWDVVDLNYEAPHNTVHKWVGEDMGTYTAARDPVFYPHHTNSD Bacillus_megaterium_tyr1 MRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGAHMSSAFLPWHREYLLRFERDLQNEVTLPYWEWEVDTGPFEQLHNRVHRWVGGQMGVPTAPNDPVFFLHHANVD Bacillus_megaterium_tyr2 MRKEYRMLTSAERDNYHNAINALKTPNMYDAVAMFHVGDAAHGGPGFLGWHRMYLVMYERALQVGVCIPYIDNTVTSGPFEYHHGSYHIHVGGLMESDTASFDPVFFMHHAYID Brugia_malayi_TYR1 MRKNVDSLSSDEVLALEKALDDLQSNQGYQAIAGYHGVPTLHGMPSFPLWHRLYVVQLERALIKTISIPYWDWTAHDNSWELAHNAIHYLVGYSMSHEYTSYDPLFFLHHSNTD Brugia_malayi_TYR2 MRKNVDTLSHDEILNLQIALRNMQGATGYQAISAYHGEPALHGMPTFPMWHRLYMVQFEQAVAGTLGIPYWDWTAKKNVFEVAHNPIHYLVGHSMSSEYTSYDPLFFLHHSNVE Brugia_malayi_TYR3 MRKSIREITESERSEYVYRVTILKKSGVYDKFVAEHHKFSIHGTDIFLPWHRIFVRKFEEEMRNNYTLPYWDWEIKTGPFERYHNRVHRFVGGDMSRHTSANDPVFWLHHCNVD Brugia_malayi_TYR4 MRKNQANLTAAEKKAFVDAVLEVKRRGIYDEFVAAHRLRFGHFGPSFLPWHRKYLIDFERELQNQVSIPYWDWTVMDGPFESMHNRVHTWVWGQMESSVSPNDPVFWLHHAFVD Caenorhabditis_briggsae_TYR1 MRKNVLRLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGAHMSSAFLPWHREYLLRFERDLQNEVTLPYWEWEVDTGPFEQLHNRVHRWVGGQMGVPTAPNDPVFFLHHANVD Caenorhabditis_briggsae_TYR2 MRKNAAHLSEEERNKFLVAIVGLKKYSVYDQFVILHMGAVGHGNPAFLSWHRMLLNKFEKALQDSVTLPYWDWTLVNSVFEKAHNPTHDWYGSTMTNACSNNDPIFWLHHCNID Caenorhabditis_briggsae_TYR3 MRKDVDSLTTAEVLALQEALKEVQGPTGYQAIAAYHGYPGIHGMPTFPQWHRLFTTQMEQALRGGIGVPYWDWTALKNYWEVAHNDIHYLVGKSMSSEYTSYDPIFFLHHSNVD Caenorhabditis_briggsae_TYR4 MRKNLLDLTDEELHDFIQGFTKFKSLFGYLNTVKWHGWPHWHQHPMFLPWHRLIMVQLELGLSMTLGIPYWDWTYVPNPFERSHSQIHNCMCYSMLTEYSCFDPTFFLHHSQID Caenorhabditis_briggsae_TYR5 MRKNQATLSADEKRRFVNALLELKRSGRYDTFVTTHNAFIGHRSPSFLPWHRRFLIEFEQALQDTVNLPYWDWTVLDGPFENLHNRVHVWVGGQMGTGVSPNDPVFWLHHAFVD Caenorhabditis_briggsae_TYR6 MRRELRSLRDEDRRMIEDAWNAMKKSGLYNKIGRVHKYSGVHSGPAFTLWHREFLKRLELALRMDFGLPFWDSTVKNGPYEFSHDYVHFFVNGDMSKYSSSNDVCFVYHHGMID Caenorhabditis_elegans_TYR1 MRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGAHMSSAFLPWHREYLLRFERDLQNEVTLPYWEWEVDTGPFEQLHNRVHRWVGGQMGVPTAPNDPVFFLHHANVD Caenorhabditis_elegans_TYR2 MRKNASSLNPIERENFCKAVLTLKALNRYDEFVAIHFGVTAHGNSGFLPWHREFLCRFEHALKDTVSLPYWDWSVNSGYFEPPHNHVHGVTVGHMGWMTSPNDPIFFLHHANVD Caenorhabditis_elegans_TYR3 MRKSVDQLTSEEILNLQKSLREVNSNLGYAAIASYHGYPTLHGSPVFPQWHRLYVVQMEQALKGSIGLPYWDWTARGNVWEVAHNTIHYLVGYSMSHEYTSYDPIFFLHHSNVD Caenorhabditis_elegans_TYR5 MRKNIRSLTEEETFDILQAMAQFKSTNGYTNIVSWHGWPYWHSDLRFCAWHRLIMVQLEMGLSLTLGIPYWDWTTYPNPFENPHNQIHRCFCYGMPITYAGWDPAFLLHHSQVE Caenorhabditis_elgans_TYR4 MRKEYRTLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNDGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFID Caenorhabditis_remanei_TYR1 MRKDANTLTAAERAEFVAAIRVLKAEGIYDRFVLRHANANIHRCSAFLPWHRRFIYDLELELQSNLGIPYWNWPVRTGPFENLHNRGHVWVGGSMLPMTSPNDPVFFMHHCMVD Caenorhabditis_remanei_TYR2 MRKNAAHLSEEERNKFLVAIVGLKKYSVYDQFVILHMGAVGHGNPAFLSWHRMLLNKFENALQDSVTLPYWDWTIVNSVFEKAHNPTHDWYGSTMTNACSNNDPIFWLHHCNID Caenorhabditis_remanei_TYR3 MRKNLLDLTDEELHDFIQGFTKFKSLFGYLNIAKWHGWPNWHNHPMFLPWHRLIMVQLELGLSMTLGIPYWDWTYVPNPFEDAHGQVHNCMCYSMLKAYSCFDSAFFLHHSQID Caenorhabditis_remanei_TYR4 MRKEYRMLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNNGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFVD Caenorhabditis_remanei_TYR5 MRKEIRMMSPSELRDLGIAMNGLKNITAWDLHTLVHYPDSAHWGPAFLPWHREFLRQFEIALQVSVTLPYWDSTVKTGPFESMHGLSHVWVGGFMYVRVSPNDPTFYMHHAFID Candidatus_nitrosopumilus_tyr MRRDCRLLDEDELSDLFGAVQDAKRPNVLDAFSFLHSRNEAHGGVGFLPFHRVFLYLYEKLLRRGVSLCFWDPTVSEGFAEELHNHVHLYIGGLMAQETAAYDPIFWFYHVYVD Ciona_intestinalis_HcB MRSAAHLVNKDYLAKYEKAVNLMKDPRSFAQQAKVHCAYCVHFSWLFFPYHRWYLYFHERILAITFALPFWNWDLVNLDFETPHGPVHAWTGEDMGNYAAARDPIFYCHHSNVD Ciona_intestinalis_HcC MRPPAQFVTDEYLEKYKLALKRMRDPRSFKQQADIHCAYCVHFSWLFFPFHRWYLYFYERILGITFALPYWNWDLVDLNYEGPHTALHRWTGEDMGRYSAGRDPIFYSHHANVD Ciona_intestinalis_HcD MRPAAHLVNDVYIAKYREALKRMKDPRNFTQQANVHCAYCVHNCWLFFPYHRWYLYFYERILGITFALPFWNWDLIDLDYEVPHGPVHSWTGENMGIYSAARDPIFFSHHANVD Ciona_intestinalis_HcE MRPAAHLADRAYLAKYERAVSLMKDPRSFEQQWRVHCAYCIHSCWLFFPWHRMYLYFHERILGITFALPFWNWDPLDLDYEVPHNPVHRWTGEDMGIYSAARDPVFFAHHGNVD Ciona_intestinalis_HcF MRRAAHLVDDDYIAKYRNAVSIMKDPRSFLSQANLHCIYCVHRSWLFFPWHRMMLYFHERILGISFALPFWNWDVVDLNYEAPHNTLHDWTGEDMGSYSAGRDPIFYGHHGNVD Ciona_intestinalis_HcG MRPAAHLVNDEYLAKYKKALDLMKDPRNFTQQANVHCAYCIHNSWLFFPFHRWYLYFYEKILGITFALPFWNWDLVDLDFEVPHGSVHLWTGEDMGTYSAARDPIFFSHHSNID Ciona_intestinalis_HcH MRPAAHLVNDEYLAKYKKALDLMKDPRNFTQQANVHCAYCVHNSWLFFPFHRWYLYFYERILGITFALPFWNWDLVDLDFEVPHGPVHLWTGENMGTYSAARDPIFYSHHSNID Ciona_intestinalis_HcI MRPAAHLVDKNYLAKYKKAIDLMKDPRNFMQQANVHCAYCVHSSWLFFPYHRWFLYFYERILGITFALPFWNWDLVDFDFEVPHGPVHLWTGENMGDYSAARDPIFYSHHSNVD Dictyostelium_discoideum_tyr1 MRRECRSLTSEEWRRLANAIRRLKPGNRFDTMARIHAMPAAHDGSSILGWHRVFLYLFENALRVGVVLCYWDSTVRTGPFEAEHNNAHVAVGALMAVPNAAWDPLFYFHHCYID Dictyostelium_discoideum_tyr2 MRQECRTLSDPDRNALFGAIVTLKGMSRYNTLAAMHNLQAAHNGPNFLGWHRVYLNMYEEALQRGVALCYWDSTVINSQFEREHDNTHVWVGGIMVNERSPEDPVFWFHHLYID Ectocarpus_siliculosus_tyr1 MRREIRDLTDRDREAFLDAMLIWYSFSNYQVITAYHNADVYHIGLQFLTSHAAFDLTMERYLQDSVSLPMWDFMIPESRFEMVHGDIHGLLGGAFSCLASPLDPLFYMLHSMFE Ectocarpus_siliculosus_tyr10 MRREIRTLTDEDREELLDAMLELWNYSDIWAINRLHFKAAFHDGLGFLTNHGLISNTFENSLQNKLTLPYWDFTVQNGRWLDPHGPVHIWIGGVMDCSSSSLDPSFWSTHPTME Ectocarpus_siliculosus_tyr11 MRREIRTLTDDEREELFDAMFALWDYADIYAINRLHYKAAFHDGLGFLTSHSMISNTFEFSLQNKLTLPYWDFTVKDGRWLDPHGPVHIWVGGVLDCASSSLDPSFWSTHPTME Ectocarpus_siliculosus_tyr12 MRREVRQLKAEDREAFLDAMEKLYDYKGISFFVQMHLDGAWHDDAGIMTHHVGYTMLFEQALQDSVTIPYWEYTVDNGRWNGTHGPVHIKMGGEWNNSSAPYDPLFWVIHPTAE Ectocarpus_siliculosus_tyr13 MRREIRSLTDKDREAFFDAMETLYEYKGINFFVQMHLNGAWHDDAGIMTHHVGYTLLFEQALQDAVTIPYWEYTVDKGRWNGTHGPVHIKVGGEWNDSSAPYDPLFWVIHPTAE Ectocarpus_siliculosus_tyr14 MRREIRDLTDRDREAFFNAVSVLQKYYSMDYFTRMHLYGGWHEGTGFMNAHMGFTLMFEQALQNSIAVPYWDFTPDRGRFGSAHGHIHEIVGGAWSMATSTIDPIFWVIHPTIE Ectocarpus_siliculosus_tyr15 MRREIRSLSDQDREMFFNAMAVMQNYYSKDYLTRLHLYYGWHQGAGFVTSHMALTLMFEQSLQNAVTVPYWDFTPTKGRFNAAHGHIHETVGGSWNHATSTNDITFWVLHPSVD Ectocarpus_siliculosus_tyr18 MRREIRTLTDRDRETFFNAVSIMQKYYSKDFFNRIHLYYGWHAGAGFVTSHIAVSLMYEQSLQNAIALPYWDFTPARGRFNGAHGEIHELLGGAWSSATSTNDPTFWLIHPTFD Ectocarpus_siliculosus_tyr2 MRREIRELTDRDREAFFDAMQTWYDFSNYMPVTAIHGTEVYHQGMQFLTSHAAFDLTMERYLQDTVSLPVWDYMVTGGRFQKIHGDIHGLLGGAFDCTASPVDPLFWVLHPLFD Ectocarpus_siliculosus_tyr3 MRREIRDLTDGDREAFLDAMETWYNYSNYMSIAAIHGTDYYHQGMQFLTSHAAFDLIVERYLQDTVSLPVWDYMVTGGRFQKIHGDIHGLLGGAFDCAASPVDPIFWVLHPLFE Ectocarpus_siliculosus_tyr4 MRREIRDLTDRDREAFFNAVSVLQKYYSMDYFTRMHLYGGWHEGTGFMNAHMGFTLMFEQALQNSIAVPYWDFTPDRGRFGSAHGHIHEIVGGAWSMATSTIDPIFWVIHPTIE Ectocarpus_siliculosus_tyr5 MRRELRDLTSADRTAFFSAMREFYTFANSKIISTYHNTRNFHSGMHFLNAHASFDLWAERSLQDTVAMHYWDFTISEGWFEQVHAANHGMMGGAFNCGPSILDPVFWALHPIFE Ectocarpus_siliculosus_tyr6 MRRELRSLTGEDRTGFFAAMREFYGFSNAKHVAAYHNSPDFHNGMHFLNAHAAFDLWVEKNLQDKVSLPQWDYMISDGWFEQVHASIHGMIGGGFDCGAAPLDPIFWTLHSGFE Ectocarpus_siliculosus_tyr7 MRRELRDLSEADREAFLDAMEAYYGFFDYQLLASYHSADLYHAGVQFLTAHAAFGLMLERSLQNRVSLPFWDYMISDGRFEKVHGDMHGLLGGAFKCGVSPMDPLFWVLHPMFE Ectocarpus_siliculosus_tyr8 MRREIRSLTDDEREELLDAMFTIWGYADIYAINRLHHKAAFHDGLGFLVSHSVLTNTFEYSLQNKLTVPYWDFTVKDGRWMAPHAPLHLWLGGTMDCSSSSYDPLFWPIHPTME Ectocarpus_siliculosus_tyr9 MRREIRTLTDDEREELFDAMFTLWDYADIYAINRLHFKAAFHDGLGFLTSHSLISNTFEYSLQNKLTLPYWDFTVKDGRWMAPHGPVHTWIGGVLNCAGSSLDPTFWPMHPTME 'Ectocarpus_siliculosus tyr16' MRQDLAAWSSSTNVLFLRALDKLQDQLSYFRLAGIHGAPSHHNDYLFPTWHRPYMLLYEQCLHMRWRLPYWDWAVNRGKYEMVHNNIHEWSGGHMANPVSSFDPVFWMHHCNVD 'Ectocarpus_siliculosus tyr17' MRYSLRELEDLPKKDFLKAWKLVKNPNSFWSIASYHGMPFQHSNVLFPTWHRFYCLRMEQALQLDVALHYWDTTVKPEGYEQPHNDIHLSIGGEMGAEVAAFDPIFFSHHSNID Glycine_max_CO1 MRKEYRMMTDNERTRWHNAIIQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPVFFLHHTFVD Glycine_max_CO10 MRRELRSLRDEDRRMIEDAWNAMKKSGLYNKIGRVHKYSGVHSGPAFTLWHREFLKRLELALRMDFGLPFWDSTVKNGPYEFSHDYVHFFVNGDMSKYSSSNDVCFVYHHGMID Glycine_max_CO11 MRQECRTLSDGARGALFGAIVDLKGMSRYDTIAGMHSFAAAHLGPSFLGWHREYLIMYEEALQRDVVLCYWDSTVINGAFEQEHDNTHVWVGEIMQDVAAPGDPVFFFHHTFID Glycine_max_CO12 MRQECRTLSDGARGALFGAIVDLKGMSRYDTIAGMHSFAAAHLGPSFLGWHRVYLIMYEEALQRDVVLCYWDSTVINGAFEQEHDNTHVWVGEIMRDVAAPGDPVFFFHHTFID Glycine_max_CO2 MRKEYRMMSDNERQRWHNALIQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPVFFLHHTFVD Glycine_max_CO3 MRKEYRMLTDQERKRFHNALIQLKRSGEYDKLALIHGRAAAHSGPAFLPWHREFIKRFEIALRDSVSIPYWDSVVTGGDFEYTHGNVHIFVGGDMYDYTSGNDPLFYLHHSFVD Glycine_max_CO4 MRKEIRMLNKNERERFFTAIQQLKASGEYNRLADIHRQEAAHAGPSFLLWHREFIKRMEIALRDSIALPYWDSSVINGPFEYYHASVHIWIGGDMKPLTSANDPVFFLHHSFVD Glycine_max_CO5 MRKEYRMLSDDERQRLHQAFRTLKQNGEYDRLARVHAQYSAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSSVNNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD Glycine_max_CO6 MRKEYRMLTDDERNRLHAAFRALKNNGEYDRIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDSVSLPYWDSTVSNGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHSFID Glycine_max_CO7 MRKEYRMLSEDERNRLHQALRTLKSNGEYDRLSRVHAQYAAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSTVTNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD Glycine_max_CO8 MRKEYRTLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNDGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFID Glycine_max_CO9 MRRELRSLRPDDRIMIENAWNAMKKSGLYNKIGRVHKYSGVHSGPAFTLWHREFLKRLELALRMDFGLPFWDSTVKNGPYEFSHDYVHFFVNGDMSKYSSSNDVCFVYHHGMID Hydra_magnipapillata_tyr MRREFSSMSREERDLYLNTFKEFSYIEIYEKFVMSHQKYFIHEAKQFYPWHRSYILKFESLLRVRVTLPFWNWAVTEGIFESWHNTIHKAIGGHMGTEYASYSPEFWSHHAMLD Illex_argentinus_tyr1 MRREVRQLKAEDREAFLDAMEKLYDYKGISFFVQMHLDGAWHDDAGIMTHHVGYTMLFEQALQDSVTIPYWEYTVDNGRWNGTHGPVHIKMGGEWNNSSAPYDPLFWVIHPTAE Illex_argentinus_tyr2 MRREIRSLTDKDREAFFDAMETLYEYKGINFFVQMHLNGAWHDDAGIMTHHVGYTLLFEQALQDAVTIPYWEYTVDKGRWNGTHGPVHIKVGGEWNDSSAPYDPLFWVIHPTAE Lottia_gigantea_Hc MRKPAHMVDEEYIAKLEKGIALMKDPRNFIQQAKVHCAYCIHRSWFFFPFHRWYLYFFERTLGINFALPFWNWDVVDLNYEAPHNTVHTWVGEDMGAYTAARDPIFYAHHPNSD Lottia_gigantea_tyr1 MRGEFTRMPYEERARYTRAFYKATYKDDFEKLLIEHSRLPHHMPQIFFPWHRWYLSKIESFLKMRVTIPYWQWTVQDGIFETFHNRFHDCVGRLMHFVTASDTPEFPLHHAFID Lottia_gigantea_tyr2 MRKDFIWMPLGDRRRFIAAFKKLTYKKEYDTIVRVHREHRIHSARYFLPWHRQFLLNLENQMRKRLTIPYWDWTVLDGPFRIFHHFVRCAIGGTACSLDSARSPEFLLITAYID Megathura_crenulata_Hc MRPAAHLVTDDYIAKYEEAVRRMQDPRSFMQQANVHRAYCVHGSWIFFPWHRWYLYFYEKILGITFALPFWNWDFIDLDYESLHNTVHSWTGHDMGLATAARDPIFFAHHSNVD Nematostella_vectensis_tyr1 MRQEIRQLEQDKELLYILGLSLMQSPVSWYGITGIHGIPHTHSSILFPTWHRPYLALYEVLLYIRFRIPYWDWAVQRAFLEAIHDTVHNLAGGHMAYPYSSFDPIFFLHHAMVD Nematostella_vectensis_tyr2 MRRELRDLQQNYPELYLLGMRDFQKLDSYYQVAGIHGMPFTHSSILFITWHRPYLALYEQALYVDFRAPYFDWATKSGDFEDVHNEIHDRTGGHMSSEVSAFDPLFWLHHVNVD Nematostella_vectensis_tyr3 MRRNINDLYARGGPLYILALSEMQEELSYFSLAGIHGLPHPHGETIFAPWHRPYVALFEQTLVATLRLPFWDWATLRCKFEDPHNTVHNNAGGTMANAWSAFDPLFMLHHANTD Nematostella_vectensis_tyr4 MRKDFESMSIPERRLYIQTLKKASYKSEYDRITKYHSDLFVHILEYFFPWHRWYLLLFENLLRDRVTVPYWDWSVTNGPLEVMHNDFHNAIGGVMSLDASANAPEFWFHHGYID Neurospora_crassa_tyr1 MRRNINDLYARGGPLYILALSEMQEELSYFSLAGIHGLPHPHGETIFASWHRPYVALFEQTLVATLRLPFWDWATLRCKFEDPHNTVHNNAGGTMANAWSAFDPLFMLHHANTD Neurospora_crassa_tyr2 MRQEIRQLEQDKELLYILGLSLMQSPVSWYGITGIHGIPHTHSSILFPTWHRPYLALYEQVLYIRFRIPYWDWAVQRAFLEAIHDTVHNLAGGHMAYPYSSFDPIFFLHHAMVD Neurospora_crassa_tyr3 MRRELRDLQQNYPELYLLGLRDFQKLDSYYQVAGIHGMPFTHSSILFITWHRPYLALYEQALYVDFRAPYFDWATKSGDFEDVHNEIHDRTGGHMSSEVSAFDPLFWLHHVNVD Neurospora_tetrasperma_tyr1 MRKEYRMLTEDERLRYHNALNVLKQRGEYDRISMEHQSVGAHSGPGFLPWHREYIKRFEIALRDTVSVPYWDSVVINGPFEYSHSNVHLWIGGHMKPEQSSNDPIFFSHHAFVD Neurospora_tetrasperma_tyr2 MRKEYRMMSDNERVRWHNAIMQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPIFFLHHTFVD Neurospora_tetrasperma_tyr3 MRKEYRMMTEDERRRWHNALNTLKRNGEYDRLSRQHLEVGAHSGPGFLPWHREYLKRVEIALRDTVFIPYWDSVVVTGPFEYSHSNIHLWIGGDMKPSTSANEPIFFMHHSFVD Nitrosomonas_europeae_tyr MRKEYRMMTNEERDNYHRAIVMLKLPNKFEIIADLHAGSVAHGGPGFLPWHRIYMMIWEEGLRVTVVVPYWDVTVTVGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Nucula_nucleus_Hc MRPPAQFVTDEYLEKYKLALKRMRDPRSFKQQADIHCAYCVHFSWIFFPFHRWYLYFYERILGITFALPYWNWDLVDLNYEGPHTAVHRWTGEDMGRYSAGRDPAFYSHHANVD Oryza_sativa_CO MRKEYRMLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNNGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFVD Pinctada_fucata_tyr1 MRKDFPSMSLEERRRFISALIRVSFIKTYDKLTHLHPKFFVHNKKNFFPWHRWFILNFENFIRDRVTVPYWDWSVIDGPFRAIHDEFHNAVGGTMMLACSSNAPEFWFHHGFLD Pinctada_fucata_tyr2 MRQECRTLSDGARGALFGAIVDLKGMSRYDTIAGMHSFAAAHLGPSFLGWHRVYLIMYEEALQRDVVLCYWDSTVINGAFEQEHDNTHVWVGEIMRDVAAPGDPVFFFHHTFID Pinctada_fucata_tyr3 MRLNILDFVKNDKFLYVRALQVLQDYSSFFQLGGIHGLPYTHGTVLFPTWHRAYESTWEQTLCADLRQPFWDWGKIEGDFEMVHNTVHFLIGGHMGSPHAAFDPIFWMHHCNVD Pinctada_fucata_tyr4 MRKDFESMSIPERRLYIQTLKKASYKSEYDRITKYHSDLFVHILEYFFPWHRWYLLLFENLLRDRVTVPYWDWSVTNGPLEVMHNDFHNAIGGVMSLDASANAPEFWFHHGYID Polysphondylium_pallidum_tyr1 MHKEYRMMTNEERENYHQAIIMLKLPNKFEVIADLHVGFIAHGGPGFLPWHRIYMMIWEEGLRISVVVPYWDVTVTSGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Sepia_officinalis_Hc MRPAAHLVTDDYIAKYEEAVRRMQDPRSFMQQANVHRAYCVHGSWIFFPWHRWYLYFYEKILGITFALPFWNWDFIDLDYESLHNTVHSWTGHDMGLATAAKDPIFFAHHSNVD Sepia_officinalis_tyr MRREFSSMSREERDLYLNTFKEFSYIEIYEKFVMSHQKYFIHEAKQFYPWHRSYILKFESLLRVRVTLPFWNWAVTEGIFESWHNTIHKAIGGHMGTEYASYSPEFWSHHAMLD Streptomyces_tsukubaensis_tyr MRKEIRMMSPSELRDLGIAMNGLKNITAWDLHTLVHYPDSAHWGPAFLPWHREFLRQFEIALQVSVTLPYWDSTVKTGPFESMHGLSHVWVGGFMYVRVSPNDPTFYMHHAFID Streptomyces_venezuelae_tyr MRKEYRMMTNEERDNYHRAIVMLKLPNKFEIIADLHAGSVAHGGPGFLPWHRIYMMIWEEGLRVTVVVPYWDVTVTVGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Vitis_vinifera_CO MRKEYRMLSEDERNRLHQAFRTLKQNGEYDRLARVHAQYSAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSTVNNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD ; END; [ The following blocks are output data for analysis step 11029 ] BEGIN TREES; TITLE alpha_NJ; LINK TAXA = TaxaForAnalysisStep11029; TREE tree_1 = [&R] (((Streptomyces_tsukubaensis_tyr:0.295675,Streptomyces_venezuelae_tyr:0.145567):0.174218,(Nitrosomonas_europeae_tyr:0.48193,(Polysphondylium_pallidum_tyr1:0.465938,(Bacillus_megaterium_tyr2:0.005917,Bacillus_megaterium_tyr1:0.003229):0.383847):0.004093):0.051118):0.045621,((Candidatus_nitrosopumilus_tyr:0.485185,(Dictyostelium_discoideum_tyr2:0.010772,Dictyostelium_discoideum_tyr1:0.006978):0.498525):0.008242,((((Glycine_max_CO2:0.005093,Glycine_max_CO1:0.003898):0.140966,((Glycine_max_CO4:0.019558,Glycine_max_CO3:0.057248):0.177793,(Vitis_vinifera_CO:0.198822,(Glycine_max_CO5:0.219667,((Glycine_max_CO7:0.021903,Glycine_max_CO6:0.008107):0.211449,((Oryza_sativa_CO:0.228181,Glycine_max_CO8:0.09846):0.031267,(Glycine_max_CO10:0.107266,(Glycine_max_CO9:0.106692,(Glycine_max_CO12:0.019505,Glycine_max_CO11:0.027418):0.009116):0.021148):0.015295):0.030872):0.041718):0.019157):0.016973):0.022178):0.927178,((Lottia_gigantea_Hc:0.701179,(Aspergillus_aculeatus_tyr:0.437431,((Agaricus_bisporus_tyr:0.537257,(Neurospora_crassa_tyr1:0.010209,Neurospora_tetrasperma_tyr1:0.0):0.491109):0.030961,((Neurospora_crassa_tyr3:0.006304,Neurospora_tetrasperma_tyr3:0.002836):0.373557,(Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.025547):0.429907):0.0679):0.042942):0.25443):0.042643,((Nucula_nucleus_Hc:0.209417,(Sepia_officinalis_Hc:0.221674,(Megathura_crenulata_Hc:0.199863,Aplysia_californica_Hc:0.199409):0.032417):0.0):0.29643,((Ciona_intestinalis_HcB:0.0,(Ciona_intestinalis_HcD:0.0,Ciona_intestinalis_HcC:0.173923):0.196514):0.226966,(Ciona_intestinalis_HcI:0.033079,(Ciona_intestinalis_HcH:0.023618,(Ciona_intestinalis_HcG:0.119993,(Ciona_intestinalis_HcF:0.048528,Ciona_intestinalis_HcE:0.07532):0.159899):0.104579):0.008844):0.065599):0.368664):0.198389):0.045815):0.199151,(((Nematostella_vectensis_tyr2:0.736387,Hydra_magnipapillata_tyr:0.463209):0.03935,(Nematostella_vectensis_tyr1:0.676148,(Nematostella_vectensis_tyr4:0.31471,Nematostella_vectensis_tyr3:0.33284):0.090858):0.075738):0.432532,((Caenorhabditis_remanei_TYR5:0.567455,((Caenorhabditis_briggsae_TYR6:0.0,Caenorhabditis_elegans_TYR5:0.037523):0.64724,(((Caenorhabditis_remanei_TYR3:0.020661,(Caenorhabditis_briggsae_TYR3:0.009394,Caenorhabditis_elegans_TYR3:0.017845):0.026161):0.173746,(Caenorhabditis_briggsae_TYR4:0.020302,(Caenorhabditis_remanei_TYR4:0.012076,Caenorhabditis_elgans_TYR4:0.014359):0.024251):0.085536):0.096498,((Brugia_malayi_TYR2:0.297824,Brugia_malayi_TYR1:0.18277):0.017823,(Brugia_malayi_TYR3:0.193722,((Brugia_malayi_TYR4:0.116055,(Caenorhabditis_elegans_TYR2:0.001964,(Caenorhabditis_briggsae_TYR2:0.010552,Caenorhabditis_remanei_TYR2:0.026415):0.016936):0.153102):0.0,((Caenorhabditis_briggsae_TYR5:1.0E-6,Caenorhabditis_briggsae_TYR1:1.0E-6):0.020124,(Caenorhabditis_elegans_TYR1:0.015324,Caenorhabditis_remanei_TYR1:0.011642):0.002524):0.161952):0.120154):0.0):0.034499):0.096514):0.050559):0.125927,(((Lottia_gigantea_tyr1:0.372849,(Sepia_officinalis_tyr:0.067933,(Illex_argentinus_tyr1:1.0E-6,Illex_argentinus_tyr2:1.0E-6):0.035902):0.404069):0.139882,(Lottia_gigantea_tyr2:0.70707,(Pinctada_fucata_tyr1:0.430468,(Pinctada_fucata_tyr4:0.151905,(Pinctada_fucata_tyr2:0.005332,Pinctada_fucata_tyr3:0.012699):0.169993):0.252389):0.099453):0.105575):0.040632,(((Ectocarpus_siliculosus_tyr6:0.193617,Ectocarpus_siliculosus_tyr5:0.281881):0.202454,(Ectocarpus_siliculosus_tyr4:0.269449,(Ectocarpus_siliculosus_tyr1:0.212544,(Ectocarpus_siliculosus_tyr3:0.054908,Ectocarpus_siliculosus_tyr2:0.100784):0.099179):0.048672):0.087512):0.356641,((Ectocarpus_siliculosus_tyr7:0.332349,(Ectocarpus_siliculosus_tyr8:0.151745,(Ectocarpus_siliculosus_tyr10:0.078218,(Ectocarpus_siliculosus_tyr11:0.06255,Ectocarpus_siliculosus_tyr9:0.061795):0.065953):0.024254):0.06507):0.324438,((Ectocarpus_siliculosus_tyr12:0.07968,Ectocarpus_siliculosus_tyr13:0.066955):0.477906,(Ectocarpus_siliculosus_tyr14:0.181637,(Ectocarpus_siliculosus_tyr15:0.13749,(Ectocarpus_siliculosus_tyr18:0.07221,('Ectocarpus_siliculosus tyr16':0.09272,'Ectocarpus_siliculosus tyr17':0.076492):0.036889):0.111004):0.01512):0.206852):0.1381):0.018644):0.570119):0.010826):0.113428):0.0):0.048105):0.045621); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61726] END;