#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; 16:20 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 11028 ] BEGIN TAXA; TITLE TaxaForAnalysisStep11028; DIMENSIONS NTAX=98; 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_HcA 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_tyr16 Ectocarpus_siliculosus_tyr17 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 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 Phragmatopoma_californica_tyr 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:M16276] TITLE Type_alpha_ML; LINK TAXA = TaxaForAnalysisStep11028; 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 MRLNILDFVKNDKFLYVRALQVLQDYSSFFQLGGIHGLPYTHGTVLFPTWHRAYESTWEQTLCADLRQPFWDWGKIEGDFEMVHNTVHFLIGGHMGSPHAAFDPIFWMHHCNVD Aplysia_californica_Hc MRKSVDQLTSEEILNLQKSLREVNSNLGYAAIASYHGYPTLHGSPVFPQWHRLYVVQMEQALKGSIGLPYWDWTARGNVWEVAHNTIHYLVGYSMSHEYTSYDPIFFLHHSNVD Aspergillus_aculeatus_tyr MRQDLAAWSSSTNVLFLRALDKLQDQLSYFRLAGIHGAPSHHNDYLFPTWHRPYMLLYEQCLHMRWRLPYWDWAVNRGKYEMVHNNIHEWSGGHMANPVSSFDPVFWMHHCNVD Bacillus_megaterium_tyr1 MRKNVLHLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGAHMSSAFLPWHREYLLRFERDLQNEVTLPYWEWEVDTGPFEQLHNRVHRWVGGQMGVPTAPNDPVFFLHHANVD Bacillus_megaterium_tyr2 MRKNVLRLTDTEKRDFVRTVLILKEKGIYDRYIAWHGAAGAHMSSAFLPWHREYLLRFERDLQNEVTLPYWEWEVDTGPFEQLHNRVHRWVGGQMGVPTAPNDPVFFLHHANVD Brugia_malayi_TYR1 MRKEYRMLTDQERKRFHNALIQLKRSGEYDKLALIHGRAAAHSGPAFLPWHREFIKRFEIALRDSVSIPYWDSVVTGGDFEYTHGNVHIFVGGDMYDYTSGNDPLFYLHHSFVD Brugia_malayi_TYR2 MRKEYRQLSEEERQRFHSALNRLKRSGDYDKIAQWHSNPKAHSGPAFLPWHREYIKRLEIALRDDVSLPYWDSTIINGFIEYSHANALVWIGGDMFHITSANDPLFFLHHVFVD Brugia_malayi_TYR3 MRKEIRMLNKNERERFFTAIQQLKASGEYNRLADIHRQEAAHAGPSFLLWHREFIKRMEIALRDSIALPYWDSSVINGPFEYYHASVHIWIGGDMKPLTSANDPVFFLHHSFVD Brugia_malayi_TYR4 MRKEYRMLTEDERLRYHNALNVLKQRGEYDRISMEHQSVGAHSGPGFLPWHREYIKRFEIALRDTVSVPYWDSVVINGPFEYSHSNVHLWIGGHMKPEQSSNDPIFFSHHAFVD Caenorhabditis_briggsae_TYR1 MRKEYRMMSDNERVRWHNAIMQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPIFFLHHTFVD Caenorhabditis_briggsae_TYR2 MRKEYRMMSEAERARWHNALNTLKRNGEYDRLSRQHLEVGAHSGPGFLPWHREYLKRFEIALRDLVFIPYWDSVVVTGPFEYSHSNIHLWIGGDMKPSTSANEPIFFMHHSFVD Caenorhabditis_briggsae_TYR3 MRKEYRMLSEDERNRLHQAFRTLKQNGEYDRLARVHAQYSAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSTVNNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD Caenorhabditis_briggsae_TYR4 MRKEYRMLTDDERNRLHAAFRALKNNGEYDRIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDSVSLPYWDSTVSNGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHSFID Caenorhabditis_briggsae_TYR5 MRKEYRMMSDNERVRWHNAIMQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPIFFLHHTFVD Caenorhabditis_briggsae_TYR6 MRRELRSLRDEDRRMIEDAWNAMKKSGLYNKIGRVHKYSGVHSGPAFTLWHREFLKRLELALRMDFGLPFWDSTVKNGPYEFSHDYVHFFVNGDMSKYSSSNDVCFVYHHGMID Caenorhabditis_elegans_TYR1 MRKEYRMMSDNERQRWHNALIQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPVFFLHHTFVD Caenorhabditis_elegans_TYR2 MRKEYRMMTEDERRRWHNALNTLKRNGEYDRLSRQHLEVGAHSGPGFLPWHREYLKRVEIALRDTVFIPYWDSVVVTGPFEYSHSNIHLWIGGDMKPSTSANEPIFFMHHSFVD Caenorhabditis_elegans_TYR3 MRKEYRMLSDDERQRLHQAFRTLKQNGEYDRLARVHAQYSAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSSVNNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD Caenorhabditis_elegans_TYR5 MRRELRSLRPDDRIMIENAWNAMKKSGLYNKIGRVHKYSGVHSGPAFTLWHREFLKRLELALRMDFGLPFWDSTVKNGPYEFSHDYVHFFVNGDMSKYSSSNDVCFVYHHGMID Caenorhabditis_elgans_TYR4 MRKEYRTLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNDGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFID Caenorhabditis_remanei_TYR1 MRKEYRMMTDNERTRWHNAIIQLKRSGEYDRLSVMHRQVGAHSGPGFLVWHREYMKRMEIALRDGISMPYWDSVLVSGPFEYTHASIHLWMGGDMKPSTSANDPVFFLHHTFVD Caenorhabditis_remanei_TYR2 MRKEYRMMSEDERRRWHNALNTLKRNGEYDRLSRQHLEVGAHSGPGFLPWHREYLKRVEIALRDLVFIPYWDSVVITGPFEYSHSNIHLWIGGDMKPSTSANEPIFFMHHSFVD Caenorhabditis_remanei_TYR3 MRKEYRMLSEDERNRLHQALRTLKSNGEYDRLSRVHAQYAAHSGPAFLPWHREFVKRMEFLIRDSLHLPYWDSTVTNGPFEYTHGNPHIYVGGDMLESTAANDPIFWMHHSFVD Caenorhabditis_remanei_TYR4 MRKEYRMLTDDERNRLHAAFRALKNNGEYERIGRIHSQMSAHSGPAFLPWHREFVKRVEFALRDTVNLPYWDSTVNNGPFEYTHGNVHIFVGGDMFDATSSNDPSFFLHHAFVD Caenorhabditis_remanei_TYR5 MRKEIRMMSPSELRDLGIAMNGLKNITAWDLHTLVHYPDSAHWGPAFLPWHREFLRQFEIALQVSVTLPYWDSTVKTGPFESMHGLSHVWVGGFMYVRVSPNDPTFYMHHAFID Candidatus_nitrosopumilus_tyr MRKNASSLNPIERENFCKAVLTLKALNRYDEFVAIHFGVTAHGNSGFLPWHREFLCRFEHALKDTVSLPYWDWSVNSGYFEPPHNHVHGVTVGHMGWMTSPNDPIFFLHHANVD Ciona_intestinalis_HcA --------------------------------------------------------------------------------EGPHNQIHMCMCYGMPTKYAAWDPIFLLHHSQID Ciona_intestinalis_HcB ------------------------------------------------------------RLNLTLGIPYWDWTTYPNPFENPHNQIHVCFCYGMPTPYAAWDPAFLLHHSQMD Ciona_intestinalis_HcC MRKNIRSLTEEETFDILQAMARFKSTDGYTNIVSWHGWPFWHVDLRFCAWHRIFMVQVEMGINLTLGIPYWDWTTYPNPF---------------------------------- Ciona_intestinalis_HcD MRKNIRSLTEEETFDILQAMAQFKSTNGYTNIVSWHGWPYWHSDLRFCAWHRLIMVQLEMGLSLTLGIPYWDWTTYPNPFENPHNQIHRCFCYGMPITYAGWDPAFLLHHSQVE Ciona_intestinalis_HcE MRKNLLDLTDEELHDFIQGFTKFKSLFGYLNTVKWHGWPHWHQHPMFLPWHRLIMVQLELGLSMTLGIPYWDWTYVPNPFERSHSQIHNCMCYSMLTEYSCFDPTFFLHHSQID Ciona_intestinalis_HcF MRKNLLDLTDEELHDFIQGFTKFKSLFGYLNIAKWHGWPNWHNHPMFLPWHRLIMVQLELGLSMTLGIPYWDWTYVPNPFEDAHGQVHNCMCYSMLKAYSCFDSAFFLHHSQID Ciona_intestinalis_HcG ------------------------------------------------------------GLSMTLGIPYWDWTYVPNPIALSHDQIHNCMCYSFDTGFSAFEPAFLLHHSQID Ciona_intestinalis_HcH ------------------------------------------------------------SLSMTLGIPYWDWTYVPNPFSFSHDQIHNCVCYSMDTDYSAFDAMFFLHHSQMD Ciona_intestinalis_HcI ----------------------------------------------FLPWHRLIMVQLELGLSMTLGIPYWDWTYVPNPFSHSHDDIHNCVCYSMVTDFAAFDALFFLHHSQMD Dictyostelium_discoideum_tyr1 MRKNAAHLSEEERNKFLVAIVGLKKYSVYDQFVILHMGAVGHGNPAFLSWHRMLLNKFENALQDSVTLPYWDWTIVNSVFEKAHNPTHDWYGSTMTNACSNNDPIFWLHHCNID Dictyostelium_discoideum_tyr2 MRKNAAHLSEEERNKFLVAIVGLKKYSVYDQFVILHMGAVGHGNPAFLSWHRMLLNKFEKALQDSVTLPYWDWTLVNSVFEKAHNPTHDWYGSTMTNACSNNDPIFWLHHCNID 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_tyr16 MRREIRDLTDRDRETFFNAVSVLQKYYSKDYFNRLHLFYGWHDGAGFVTSHIALSLMYEQALQSSIALPYWDFTPSRGRFNGAHGHIHELLGGAWSSGTSTNDVTFWVLHPTMD Ectocarpus_siliculosus_tyr17 MRREIRSLTDRDRETFFNAVAVLQKYYSKDYFNRMHLYYGWHAGAGFVTSHIAITLMYEQALQNSIALPYWDVTPTQGRFNGAHGNIHGLLGGTWSPATSTNDVTFWVLHPTFD Ectocarpus_siliculosus_tyr18 MRREIRTLTDRDRETFFNAVSIMQKYYSKDFFNRIHLYYGWHAGAGFVTSHIAVSLMYEQSLQNAIALPYWDFTPARGRFNGAHGEIHELLGGAWSSATSTNDPTFWLIHPTFD Ectocarpus_siliculosus_tyr2 MRREIRELTDRDREAFFDAMQTWYDFSNYMPVTAIHGTEVYHQGMQFLTSHAAFDLTMERYLQDTVSLPVWDYMVTGGRFQKIHGDIHGLLGGAFDCTASPVDPLFWVLHPLFD Ectocarpus_siliculosus_tyr3 MRREIRDLTDGDREAFLDAMETWYNYSNYMSIAAIHGTDYYHQGMQFLTSHAAFDLIVERYLQDTVSLPVWDYMVTGGRFQKIHGDIHGLLGGAFDCAASPVDPIFWVLHPLFE Ectocarpus_siliculosus_tyr4 MRRELRDLSEADREAFLDAMEAYYGFFDYQLLASYHSADLYHAGVQFLTAHAAFGLMLERSLQNRVSLPFWDYMISDGRFEKVHGDMHGLLGGAFKCGVSPMDPLFWVLHPMFE Ectocarpus_siliculosus_tyr5 MRRELRDLTSADRTAFFSAMREFYTFANSKIISTYHNTRNFHSGMHFLNAHASFDLWAERSLQDTVAMHYWDFTISEGWFEQVHAANHGMMGGAFNCGPSILDPVFWALHPIFE Ectocarpus_siliculosus_tyr6 MRRELRSLTGEDRTGFFAAMREFYGFSNAKHVAAYHNSPDFHNGMHFLNAHAAFDLWVEKNLQDKVSLPQWDYMISDGWFEQVHASIHGMIGGGFDCGAAPLDPIFWTLHSGFE Ectocarpus_siliculosus_tyr7 MRREIRSLFDDERDQMFDAMKVLWDYLDVWTIDQFHQIGALHDGIGFGITHSMVTMMFENSLQNMLSLPYWDFTVKDGRWQGPHGPVHVWVGGNVDCSSSPLDPTFWSMHPTME Ectocarpus_siliculosus_tyr8 MRREIRSLTDDEREELLDAMFTIWGYADIYAINRLHHKAAFHDGLGFLVSHSVLTNTFEYSLQNKLTVPYWDFTVKDGRWMAPHAPLHLWLGGTMDCSSSSYDPLFWPIHPTME Ectocarpus_siliculosus_tyr9 MRREIRTLTDDEREELFDAMFTLWDYADIYAINRLHFKAAFHDGLGFLTSHSLISNTFEYSLQNKLTLPYWDFTVKDGRWMAPHGPVHTWIGGVLNCAGSSLDPTFWPMHPTME Glycine_max_CO1 MRPAAHLVTDDYIAKYEEAVRRMQDPRSFMQQANVHRAYCVHGSWIFFPWHRWYLYFYEKILGITFALPFWNWDFIDLDYESLHNTVHSWTGHDMGLATAARDPIFFAHHSNVD Glycine_max_CO10 MRPAAHLVNDVYIAKYREALKRMKDPRNFTQQANVHCAYCVHNCWLFFPYHRWYLYFYERILGITFALPFWNWDLIDLDYEVPHGPVHSWTGENMGIYSAARDPIFFSHHANVD Glycine_max_CO11 MRPAAHLVNDEYLAKYKKALDLMKDPRNFTQQANVHCAYCVHNSWLFFPFHRWYLYFYERILGITFALPFWNWDLVDLDFEVPHGPVHLWTGENMGTYSAARDPIFYSHHSNID Glycine_max_CO12 MRPAAHLVNDEYLAKYKKALDLMKDPRNFTQQANVHCAYCIHNSWLFFPFHRWYLYFYEKILGITFALPFWNWDLVDLDFEVPHGSVHLWTGEDMGTYSAARDPIFFSHHSNID Glycine_max_CO2 MRPAAHLVTDDYIAKYEEAVRRMQDPRSFMQQANVHRAYCVHGSWIFFPWHRWYLYFYEKILGITFALPFWNWDFIDLDYESLHNTVHSWTGHDMGLATAAKDPIFFAHHSNVD Glycine_max_CO3 MRKPAHMVDEEYIAKLEKGIALMKDPRNFIQQAKVHCAYCIHRSWFFFPFHRWYIYFFERILGLNFALPFWNWDVVDLNYEAPHNTVHKWVGEDMGTYTAARDPVFYPHHTNSD Glycine_max_CO4 MRKPAHMVDEEYIAKLEKGIALMKDPRNFIQQAKVHCAYCIHRSWFFFPFHRWYLYFFERTLGINFALPFWNWDVVDLNYEAPHNTVHTWVGEDMGAYTAARDPIFYAHHPNSD Glycine_max_CO5 MRRPAQWVDDDYLNKYKEAVRLMRDPRNFMQQAKIHCAYCVHGNWLFAPFHRWYLYFHERILGITFALPFWNWDIVDLANEGPHNNVHRWTGIDMGYAWAARDPIFFAHHSNVD Glycine_max_CO6 MRPPAQFVTDEYLEKYKLALKRMRDPRSFKQQADIHCAYCVHFSWIFFPFHRWYLYFYERILGITFALPYWNWDLVDLNYEGPHTAVHRWTGEDMGRYSAGRDPAFYSHHANVD Glycine_max_CO7 MRPPAQFVTDEYLEKYKLALKRMRDPRSFKQQADIHCAYCVHFSWLFFPFHRWYLYFYERILGITFALPYWNWDLVDLNYEGPHTALHRWTGEDMGRYSAGRDPIFYSHHANVD Glycine_max_CO8 MRSAAHLVNKDYLAKYEKAVNLMKDPRSFAQQAKVHCAYCVHFSWLFFPYHRWYLYFHERILAITFALPFWNWDLVNLDFETPHGPVHAWTGEDMGNYAAARDPIFYCHHSNVD Glycine_max_CO9 MRPAAHLVDKNYLAKYKKAIDLMKDPRNFMQQANVHCAYCVHSSWLFFPYHRWFLYFYERILGITFALPFWNWDLVDFDFEVPHGPVHLWTGENMGDYSAARDPIFYSHHSNVD Hydra_magnipapillata_tyr MRREFSSMSREERDLYLNTFKEFSYIEIYEKFVMSHQKYFIHEAKQFYPWHRSYILKFESLLRVRVTLPFWNWAVTEGIFESWHNTIHKAIGGHMGTEYASYSPEFWSHHAMLD Illex_argentinus_tyr1 MRKEYRMMTNEERDNYHRAIVMLKLPNKFEIIADLHAGSVAHGGPGFLPWHRIYMMIWEEGLRVTVVVPYWDVTVTVGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Illex_argentinus_tyr2 MRKEYRMMTNEERDNYHRAIVMLKLPNKFEIIADLHAGSVAHGGPGFLPWHRIYMMIWEEGLRVTVVVPYWDVTVTVGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Lottia_gigantea_Hc MRYSLRELEDLPKKDFLKAWKLVKNPNSFWSIASYHGMPFQHSNVLFPTWHRFYCLRMEQALQLDVALHYWDTTVKPEGYEQPHNDIHLSIGGEMGAEVAAFDPIFFSHHSNID Lottia_gigantea_tyr1 MRKEYRMLTSAERDNYHNAINALKTPNMYDAVAMFHVGDAAHGGPGFLGWHRMYLVMYERALQVGVCIPYIDNTVTSGPFEYHHGSYHIHVGGLMESDTASFDPVFFMHHAYID Lottia_gigantea_tyr2 MRRDCRLLDEDELSDLFGAVQDAKRPNVLDAFSFLHSRNEAHGGVGFLPFHRVFLYLYEKLLRRGVSLCFWDPTVSEGFAEELHNHVHLYIGGLMAQETAAYDPIFWFYHVYVD Megathura_crenulata_Hc MRKNVDSLSSDEVLALEKALDDLQSNQGYQAIAGYHGVPTLHGMPSFPLWHRLYVVQLERALIKTISIPYWDWTAHDNSWELAHNAIHYLVGYSMSHEYTSYDPLFFLHHSNTD Nematostella_vectensis_tyr1 MRKDFIWMPLGDRRRFIAAFKKLTYKKEYDTIVRVHREHRIHSARYFLPWHRQFLLNLENQMRKRLTIPYWDWTVLDGPFRIFHHFVRCAIGGTACSLDSARSPEFLLITAYID Nematostella_vectensis_tyr2 MRGEFTRMPYEERARYTRAFYKATYKDDFEKLLIEHSRLPHHMPQIFFPWHRWYLSKIESFLKMRVTIPYWQWTVQDGIFETFHNRFHDCVGRLMHFVTASDTPEFPLHHAFID Nematostella_vectensis_tyr3 MRKDFPSMSLEERRRFISALIRVSFIKTYDKLTHLHPKFFVHNKKNFFPWHRWFILNFENFIRDRVTVPYWDWSVIDGPFRAIHDEFHNAVGGTMMLACSSNAPEFWFHHGFLD Nematostella_vectensis_tyr4 MRKDFESMSIPERRLYIQTLKKASYKSEYDRITKYHSDLFVHILEYFFPWHRWYLLLFENLLRDRVTVPYWDWSVTNGPLEVMHNDFHNAIGGVMSLDASANAPEFWFHHGYID Neurospora_crassa_tyr1 MRRNINDLYARGGPLYILALSEMQEELSYFSLAGIHGLPHPHGETIFASWHRPYVALFEQTLVATLRLPFWDWATLRCKFEDPHNTVHNNAGGTMANAWSAFDPLFMLHHANTD Neurospora_crassa_tyr2 MRQEIRQLEQDKELLYILGLSLMQSPVSWYGITGIHGIPHTHSSILFPTWHRPYLALYEQVLYIRFRIPYWDWAVQRAFLEAIHDTVHNLAGGHMAYPYSSFDPIFFLHHAMVD Neurospora_crassa_tyr3 MRRELRDLQQNYPELYLLGLRDFQKLDSYYQVAGIHGMPFTHSSILFITWHRPYLALYEQALYVDFRAPYFDWATKSGDFEDVHNEIHDRTGGHMSSEVSAFDPLFWLHHVNVD Neurospora_tetrasperma_tyr1 MRRNINDLYARGGPLYILALSEMQEELSYFSLAGIHGLPHPHGETIFAPWHRPYVALFEQTLVATLRLPFWDWATLRCKFEDPHNTVHNNAGGTMANAWSAFDPLFMLHHANTD Neurospora_tetrasperma_tyr2 MRQEIRQLEQDKELLYILGLSLMQSPVSWYGITGIHGIPHTHSSILFPTWHRPYLALYEVLLYIRFRIPYWDWAVQRAFLEAIHDTVHNLAGGHMAYPYSSFDPIFFLHHAMVD Neurospora_tetrasperma_tyr3 MRRELRDLQQNYPELYLLGMRDFQKLDSYYQVAGIHGMPFTHSSILFITWHRPYLALYEQALYVDFRAPYFDWATKSGDFEDVHNEIHDRTGGHMSSEVSAFDPLFWLHHVNVD Nitrosomonas_europeae_tyr MRKDANTLTAAERAEFVAAIRVLKAEGIYDRFVLRHANANIHRCSAFLPWHRRFIYDLELELQSNLGIPYWNWPVRTGPFENLHNRGHVWVGGSMLPMTSPNDPVFFMHHCMVD Nucula_nucleus_Hc MRKDVDSLTTAEVLALQEALKEVQGPTGYQAIAAYHGYPGIHGMPTFPQWHRLFTTQMEQALRGGIGVPYWDWTALKNYWEVAHNDIHYLVGKSMSSEYTSYDPIFFLHHSNVD Oryza_sativa_CO MRPAAHLADRAYLAKYERAVSLMKDPRSFEQQWRVHCAYCIHSCWLFFPWHRMYLYFHERILGITFALPFWNWDPLDLDYEVPHNPVHRWTGEDMGIYSAARDPVFFAHHGNVD Phragmatopoma_californica_tyr MRKAYRHLSDSERKDFHDAIYQLKDLSNYDLFVNLHRSNSAHGGHAFAGWHRHCLYRFEKALQNDVTLCYLDTT---------------------------------------- Pinctada_fucata_tyr1 MRRECRSLTSEEWRRLANAIRRLKPGNRFDTMARIHAMPAAHDGSSILGWHRVFLYLFENALRVGVVLCYWDSTVRTGPFEAEHNNAHVAVGALMAVPNAAWDPLFYFHHCYID Pinctada_fucata_tyr2 MRQECRTLSDGARGALFGAIVDLKGMSRYDTIAGMHSFAAAHLGPSFLGWHRVYLIMYEEALQRDVVLCYWDSTVINGAFEQEHDNTHVWVGEIMRDVAAPGDPVFFFHHTFID Pinctada_fucata_tyr3 MRQECRTLSDGARGALFGAIVDLKGMSRYDTIAGMHSFAAAHLGPSFLGWHREYLIMYEEALQRDVVLCYWDSTVINGAFEQEHDNTHVWVGEIMQDVAAPGDPVFFFHHTFID Pinctada_fucata_tyr4 MRQECRTLSDPDRNALFGAIVTLKGMSRYNTLAAMHNLQAAHNGPNFLGWHRVYLNMYEEALQRGVALCYWDSTVINSQFEREHDNTHVWVGGIMVNERSPEDPVFWFHHLYID Polysphondylium_pallidum_tyr1 MRKSIREITESERSEYVYRVTILKKSGVYDKFVAEHHKFSIHGTDIFLPWHRIFVRKFEEEMRNNYTLPYWDWEIKTGPFERYHNRVHRFVGGDMSRHTSANDPVFWLHHCNVD Sepia_officinalis_Hc MRKNVDTLSHDEILNLQIALRNMQGATGYQAISAYHGEPALHGMPTFPMWHRLYMVQFEQAVAGTLGIPYWDWTAKKNVFEVAHNPIHYLVGHSMSSEYTSYDPLFFLHHSNVE Sepia_officinalis_tyr MHKEYRMMTNEERENYHQAIIMLKLPNKFEVIADLHVGFIAHGGPGFLPWHRIYMMIWEEGLRISVVVPYWDVTVTSGPFELYHNNIHDWIGGTVSVAWASFDPAFMLIHGYVD Streptomyces_tsukubaensis_tyr MRKNQANLTAAEKKAFVDAVLEVKRRGIYDEFVAAHRLRFGHFGPSFLPWHRKYLIDFERELQNQVSIPYWDWTVMDGPFESMHNRVHTWVWGQMESSVSPNDPVFWLHHAFVD Streptomyces_venezuelae_tyr MRKNQATLSADEKRRFVNALLELKRSGRYDTFVTTHNAFIGHRSPSFLPWHRRFLIEFEQALQDTVNLPYWDWTVLDGPFENLHNRVHVWVGGQMGTGVSPNDPVFWLHHAFVD Vitis_vinifera_CO MRRAAHLVDDDYIAKYRNAVSIMKDPRSFLSQANLHCIYCVHRSWLFFPWHRMMLYFHERILGISFALPFWNWDVVDLNYEAPHNTLHDWTGEDMGSYSAGRDPIFYGHHGNVD ; END; [ The following blocks are output data for analysis step 11028 ] BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_17 = [&R] ((((((((((((Brugia_malayi_TYR3:0.368594,((((Caenorhabditis_briggsae_TYR2:0.005185,(Caenorhabditis_remanei_TYR2:1.0E-6,Caenorhabditis_elegans_TYR2:0.011715):0.033194):0.128113,(((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.056916,Caenorhabditis_remanei_TYR1:0.011374):0.034239,Caenorhabditis_elegans_TYR1:1.0E-6):0.314089):0.041842,Brugia_malayi_TYR4:0.108849):0.116618,Brugia_malayi_TYR2:0.3468):3.0E-6):7.0E-6,(((Nematostella_vectensis_tyr2:1.041385,Hydra_magnipapillata_tyr:0.749618):0.305769,(Nematostella_vectensis_tyr3:0.29389,Nematostella_vectensis_tyr4:0.386931):0.370362):0.148072,Nematostella_vectensis_tyr1:0.924433):1.24803):0.113694,(Brugia_malayi_TYR1:0.204446,(((Caenorhabditis_elegans_TYR5:0.038741,Caenorhabditis_briggsae_TYR6:0.0):1.0158,((Caenorhabditis_remanei_TYR4:0.01083,Caenorhabditis_elgans_TYR4:0.034917):0.046031,Caenorhabditis_briggsae_TYR4:0.0):6.0E-6):0.094881,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.044911):0.022179,Caenorhabditis_elegans_TYR3:0.034284):0.233144):0.105611):0.039016):0.375153,(Caenorhabditis_remanei_TYR5:0.5154,(Phragmatopoma_californica_tyr:0.435099,(((((Streptomyces_tsukubaensis_tyr:0.311564,Nitrosomonas_europeae_tyr:0.685859):0.102544,Streptomyces_venezuelae_tyr:0.173476):0.372562,(Dictyostelium_discoideum_tyr1:0.0,Dictyostelium_discoideum_tyr2:0.02402):0.517384):0.173709,Candidatus_nitrosopumilus_tyr:0.748361):0.122647,((Bacillus_megaterium_tyr1:1.0E-6,Bacillus_megaterium_tyr2:0.011626):0.324163,Polysphondylium_pallidum_tyr1:0.758342):0.174616):0.231302):0.080697):0.10924):0.166195,(((Lottia_gigantea_Hc:0.13631,Ciona_intestinalis_HcA:0.905333):1.284155,((((((Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.036923):0.018966,(Glycine_max_CO9:0.04783,Glycine_max_CO8:0.316076):0.130237):0.091123,((Glycine_max_CO7:1.0E-6,Glycine_max_CO6:0.031428):0.368663,Glycine_max_CO10:0.054254):0.032546):0.189402,(Glycine_max_CO5:0.386948,(Glycine_max_CO2:0.012211,Glycine_max_CO1:1.0E-6):0.147594):0.092193):0.060648,(Oryza_sativa_CO:0.312868,Vitis_vinifera_CO:0.136911):0.134783):0.140749,(Glycine_max_CO4:0.049455,Glycine_max_CO3:0.071027):0.16766):1.860583):0.255485,((((Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.035336):0.212528,Pinctada_fucata_tyr4:0.226163):0.2615,(Lottia_gigantea_tyr2:0.994967,Pinctada_fucata_tyr1:0.612049):0.118803):0.306459,(((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.066631,Sepia_officinalis_tyr:0.051799):0.825597,Lottia_gigantea_tyr1:0.264821):0.113452):3.0E-6):0.247402):0.383116,((Ciona_intestinalis_HcH:0.065551,((Ciona_intestinalis_HcE:2.26E-4,(Ciona_intestinalis_HcG:0.17587,Ciona_intestinalis_HcF:0.094149):0.059637):0.277534,((Ciona_intestinalis_HcD:0.07992,(Ciona_intestinalis_HcB:0.053432,Ciona_intestinalis_HcC:0.120655):0.160519):0.332179,Ciona_intestinalis_HcI:0.110149):0.125989):0.017386):0.837306,((Aplysia_californica_Hc:0.260136,(Nucula_nucleus_Hc:0.220757,Megathura_crenulata_Hc:0.45081):0.041403):0.201168,Sepia_officinalis_Hc:0.261509):0.709475):0.594336):0.022948,(((Ectocarpus_siliculosus_tyr15:0.249762,((Ectocarpus_siliculosus_tyr17:0.149338,Ectocarpus_siliculosus_tyr18:0.157673):0.050884,Ectocarpus_siliculosus_tyr16:0.069752):0.264242):0.120579,Ectocarpus_siliculosus_tyr14:0.209593):0.230516,(((Ectocarpus_siliculosus_tyr7:0.131808,((Ectocarpus_siliculosus_tyr9:0.018626,Ectocarpus_siliculosus_tyr8:0.299529):0.087379,(Ectocarpus_siliculosus_tyr10:0.301316,Ectocarpus_siliculosus_tyr11:2.0E-6):0.09153):0.203987):0.585306,((Ectocarpus_siliculosus_tyr4:0.213822,((Ectocarpus_siliculosus_tyr2:0.052382,Ectocarpus_siliculosus_tyr3:0.133793):0.160009,Ectocarpus_siliculosus_tyr1:0.198239):0.142227):0.192009,(Ectocarpus_siliculosus_tyr5:0.381677,Ectocarpus_siliculosus_tyr6:0.276119):0.234572):0.558665):0.207437,(Ectocarpus_siliculosus_tyr12:0.229808,Ectocarpus_siliculosus_tyr13:2.0E-6):0.736475):0.326545):0.796719):1.304139,Aspergillus_aculeatus_tyr:0.60802):0.361368,(Neurospora_tetrasperma_tyr2:0.011558,Neurospora_crassa_tyr2:0.0):0.417382):0.126598,(Neurospora_tetrasperma_tyr3:0.023541,Neurospora_crassa_tyr3:1.0E-6):0.738129):0.230373,Agaricus_bisporus_tyr:1.459541):0.596736,Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61713] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_14 = [&R] (((((((((((((((((Brugia_malayi_TYR1:0.206433,(((Caenorhabditis_elegans_TYR5:0.015102,Caenorhabditis_briggsae_TYR6:0.012902):1.109716,(Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_elgans_TYR4:0.042834,Caenorhabditis_remanei_TYR4:0.0):0.025171):3.0E-6):0.118597,(Caenorhabditis_remanei_TYR3:0.040319,(Caenorhabditis_elegans_TYR3:0.00846,Caenorhabditis_briggsae_TYR3:0.0):0.034563):0.207788):0.123242):0.027245,((((((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):1.5E-5,(Caenorhabditis_elegans_TYR1:0.0088,Caenorhabditis_remanei_TYR1:0.0):0.035526):0.118482,((Caenorhabditis_remanei_TYR2:0.018172,Caenorhabditis_elegans_TYR2:0.0):0.0015,Caenorhabditis_briggsae_TYR2:0.02786):0.137505):0.101821,Brugia_malayi_TYR4:0.261885):0.083883,Brugia_malayi_TYR3:0.243383):0.108507,Brugia_malayi_TYR2:0.353631):0.035747):0.030437,Caenorhabditis_remanei_TYR5:1.078923):0.174023,((((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.041534,Sepia_officinalis_tyr:0.071368):0.597675,Lottia_gigantea_tyr1:0.352712):0.276473,((((Pinctada_fucata_tyr3:0.026474,Pinctada_fucata_tyr2:2.6E-5):0.17074,Pinctada_fucata_tyr4:0.254646):0.402009,Pinctada_fucata_tyr1:0.732037):0.143574,Lottia_gigantea_tyr2:0.882782):0.241346):0.223541):0.396963,(((Nematostella_vectensis_tyr3:0.193118,Nematostella_vectensis_tyr1:1.047442):0.079453,(Nematostella_vectensis_tyr4:0.320754,(Nematostella_vectensis_tyr2:0.71615,Hydra_magnipapillata_tyr:0.692443):0.336784):0.057665):1.159065,((((Ectocarpus_siliculosus_tyr7:0.133439,(Ectocarpus_siliculosus_tyr10:0.23336,((Ectocarpus_siliculosus_tyr9:0.080342,Ectocarpus_siliculosus_tyr8:0.298326):0.107666,Ectocarpus_siliculosus_tyr11:0.006176):0.031119):0.304341):0.968962,(((Ectocarpus_siliculosus_tyr16:0.026075,((Ectocarpus_siliculosus_tyr15:0.248499,Ectocarpus_siliculosus_tyr17:0.110073):0.020765,Ectocarpus_siliculosus_tyr18:0.12081):0.042963):0.131959,Ectocarpus_siliculosus_tyr14:0.119611):0.328011,(Ectocarpus_siliculosus_tyr13:3.0E-6,Ectocarpus_siliculosus_tyr12:0.223109):0.595971):0.412017):0.350105,((Ectocarpus_siliculosus_tyr3:0.126963,Ectocarpus_siliculosus_tyr2:0.065555):0.159905,Ectocarpus_siliculosus_tyr1:0.272257):0.039578):0.113812,((Ectocarpus_siliculosus_tyr6:0.210542,Ectocarpus_siliculosus_tyr5:0.275744):0.265274,Ectocarpus_siliculosus_tyr4:0.335768):6.0E-6):1.6793):0.225716):0.098146,((Streptomyces_tsukubaensis_tyr:0.248702,((Phragmatopoma_californica_tyr:1.212723,(Nitrosomonas_europeae_tyr:0.814758,(((Bacillus_megaterium_tyr1:0.0,Bacillus_megaterium_tyr2:0.027719):0.318237,Polysphondylium_pallidum_tyr1:0.835996):0.076479,Candidatus_nitrosopumilus_tyr:0.751721):4.0E-6):1.8E-5):0.333195,(Dictyostelium_discoideum_tyr1:0.008324,Dictyostelium_discoideum_tyr2:0.0):0.800224):0.340004):0.211641,Streptomyces_venezuelae_tyr:2.0E-6):0.231491):0.862179,(((Nucula_nucleus_Hc:0.241301,Sepia_officinalis_Hc:0.18531):0.122168,Aplysia_californica_Hc:0.191384):0.11185,Megathura_crenulata_Hc:0.09286):0.608799):0.391977,((Ciona_intestinalis_HcF:0.109297,Ciona_intestinalis_HcE:0.033665):0.079362,((Ciona_intestinalis_HcI:0.205073,Ciona_intestinalis_HcH:2.0E-6):0.098136,Ciona_intestinalis_HcG:0.136823):0.071348):0.218019):0.238063,((Ciona_intestinalis_HcC:0.050188,Ciona_intestinalis_HcD:0.081995):0.069544,Ciona_intestinalis_HcB:0.016005):0.097352):0.201586,Ciona_intestinalis_HcA:2.2E-5):0.800651,Lottia_gigantea_Hc:0.856905):0.234661,((((Glycine_max_CO5:0.170537,(Glycine_max_CO7:0.02024,Glycine_max_CO6:0.02303):0.153144):0.121691,(Glycine_max_CO3:0.070009,Glycine_max_CO4:0.019839):0.118073):0.073005,Vitis_vinifera_CO:0.198812):0.023418,((((((Glycine_max_CO12:0.028296,Glycine_max_CO11:0.0):0.014985,Glycine_max_CO9:0.085924):0.038254,Glycine_max_CO10:0.115029):0.078404,Glycine_max_CO8:0.115714):0.033224,Oryza_sativa_CO:0.195388):0.027254,(Glycine_max_CO2:0.0,Glycine_max_CO1:0.0):0.197387):2.0E-6):1.834455):0.258824,Agaricus_bisporus_tyr:0.314173):0.400677,(Neurospora_tetrasperma_tyr1:0.009074,Neurospora_crassa_tyr1:0.0):0.407739):0.175026,Aspergillus_aculeatus_tyr:0.919472):0.08531,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.0):0.61667):0.554449,Neurospora_tetrasperma_tyr2:0.008329,Neurospora_crassa_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61710] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_27 = [&R] ((((((((((((((Brugia_malayi_TYR2:0.194454,(((Brugia_malayi_TYR4:0.204984,(Caenorhabditis_briggsae_TYR2:0.038308,(Caenorhabditis_remanei_TYR2:0.008825,Caenorhabditis_elegans_TYR2:0.0):0.021478):0.118875):0.076805,((((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.007877,Caenorhabditis_remanei_TYR1:1.0E-6):0.015991,Caenorhabditis_elegans_TYR1:0.0):0.104425,Brugia_malayi_TYR3:0.251923):0.092578):0.149564,Brugia_malayi_TYR1:0.140013):0.091818):2.0E-6,((Caenorhabditis_elegans_TYR3:0.029199,(Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.053735):0.014764):0.166707,(Caenorhabditis_remanei_TYR4:0.0,((Caenorhabditis_elgans_TYR4:0.008515,Caenorhabditis_briggsae_TYR4:0.00848):1.0E-6,(Caenorhabditis_briggsae_TYR6:0.012727,Caenorhabditis_elegans_TYR5:0.041474):0.614241):0.008489):0.083921):0.216468):0.051304,Caenorhabditis_remanei_TYR5:1.273652):0.43092,(((((Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.037026):0.292498,Pinctada_fucata_tyr4:0.147136):0.413765,Pinctada_fucata_tyr1:0.715068):0.097973,Lottia_gigantea_tyr2:0.707634):0.167026,(((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.016787,Sepia_officinalis_tyr:0.031982):0.527699,Lottia_gigantea_tyr1:0.457597):0.132235):0.114714):0.03583,((((Hydra_magnipapillata_tyr:1.245675,Nematostella_vectensis_tyr3:0.221991):0.226477,Nematostella_vectensis_tyr2:1.079719):0.302803,Nematostella_vectensis_tyr4:0.418362):0.139537,Nematostella_vectensis_tyr1:0.568922):1.00345):0.125316,(((((Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.564953,Polysphondylium_pallidum_tyr1:0.593875):0.059784,Nitrosomonas_europeae_tyr:0.792859):0.274834,(((Dictyostelium_discoideum_tyr2:1.0E-6,Dictyostelium_discoideum_tyr1:0.017653):0.542457,Candidatus_nitrosopumilus_tyr:0.651898):4.7E-5,(Streptomyces_venezuelae_tyr:0.008263,Streptomyces_tsukubaensis_tyr:0.515147):0.590902):0.056173):0.183174,Phragmatopoma_californica_tyr:0.244469):0.230381):5.0E-6,(Glycine_max_CO2:3.0E-6,(Glycine_max_CO1:1.0E-6,((Glycine_max_CO3:0.047738,Glycine_max_CO4:0.037929):0.201145,((((Oryza_sativa_CO:0.199402,Glycine_max_CO8:0.100843):0.038177,Glycine_max_CO5:0.218602):0.035824,((Glycine_max_CO9:0.072707,(Glycine_max_CO10:0.123534,(Glycine_max_CO12:0.035946,Glycine_max_CO11:0.0):0.008463):0.038122):0.053535,(Glycine_max_CO7:0.0,Glycine_max_CO6:0.009476):0.187653):0.025141):0.062957,Vitis_vinifera_CO:0.10976):0.026657):0.141125):0.008822):1.100504):0.23044,((((Ectocarpus_siliculosus_tyr9:0.065056,(Ectocarpus_siliculosus_tyr10:0.165134,Ectocarpus_siliculosus_tyr11:0.051532):0.026269):0.066133,Ectocarpus_siliculosus_tyr8:0.111541):0.139464,Ectocarpus_siliculosus_tyr7:0.159373):0.16651,((((Ectocarpus_siliculosus_tyr6:0.290132,Ectocarpus_siliculosus_tyr5:0.307069):0.257785,Ectocarpus_siliculosus_tyr4:0.335383):0.05943,((Ectocarpus_siliculosus_tyr2:0.037991,Ectocarpus_siliculosus_tyr3:0.131728):0.144497,Ectocarpus_siliculosus_tyr1:0.112783):0.135958):0.698996,((((Ectocarpus_siliculosus_tyr13:1.0E-6,Ectocarpus_siliculosus_tyr12:0.160037):0.502777,Ectocarpus_siliculosus_tyr14:0.044444):0.083981,(Ectocarpus_siliculosus_tyr17:0.048663,(Ectocarpus_siliculosus_tyr16:0.062378,Ectocarpus_siliculosus_tyr18:0.07936):0.054587):0.189169):0.191756,Ectocarpus_siliculosus_tyr15:0.119197):0.455823):0.149245):0.755096):0.302627,Lottia_gigantea_Hc:0.727568):0.024301,((((Megathura_crenulata_Hc:0.242066,Aplysia_californica_Hc:0.134224):0.113515,Nucula_nucleus_Hc:0.191656):0.10131,Sepia_officinalis_Hc:0.138355):0.263298,(((Ciona_intestinalis_HcG:0.189405,((((Ciona_intestinalis_HcB:0.130889,Ciona_intestinalis_HcC:0.079281):0.031905,Ciona_intestinalis_HcD:0.027369):0.142245,Ciona_intestinalis_HcA:0.068987):0.205545,(Ciona_intestinalis_HcE:0.094985,Ciona_intestinalis_HcF:0.048978):0.244437):0.041997):0.061852,Ciona_intestinalis_HcI:0.125153):0.142392,Ciona_intestinalis_HcH:2.25E-4):0.640649):0.336561):0.402582,((Neurospora_crassa_tyr3:1.0E-6,Neurospora_tetrasperma_tyr3:0.008321):0.448915,(Neurospora_tetrasperma_tyr2:0.045619,Neurospora_crassa_tyr2:1.0E-6):0.42583):0.242627):0.143362,Aspergillus_aculeatus_tyr:0.381144):0.155888,Agaricus_bisporus_tyr:0.74414):0.573364,Neurospora_tetrasperma_tyr1:0.009253,Neurospora_crassa_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61723] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_1000 = [&R] ((((((((((((((((Brugia_malayi_TYR2:0.340364,((((Caenorhabditis_briggsae_TYR6:0.025462,Caenorhabditis_elegans_TYR5:0.0):0.912677,((Caenorhabditis_remanei_TYR4:0.0,Caenorhabditis_elgans_TYR4:0.016984):0.033951,Caenorhabditis_briggsae_TYR4:0.0):0.031957):0.060457,((Caenorhabditis_elegans_TYR3:0.008452,Caenorhabditis_briggsae_TYR3:0.0):1.0E-6,Caenorhabditis_remanei_TYR3:0.03492):0.220517):0.165476,Brugia_malayi_TYR1:0.165574):0.042875):0.059532,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):1.0E-6,(Caenorhabditis_remanei_TYR1:0.0,Caenorhabditis_elegans_TYR1:0.0):0.016507):0.158686,((Caenorhabditis_briggsae_TYR2:1.0E-6,(Caenorhabditis_remanei_TYR2:0.0,Caenorhabditis_elegans_TYR2:0.0):0.00878):0.118972,Brugia_malayi_TYR4:0.11233):0.058546):0.123245):4.0E-6,(((Sepia_officinalis_tyr:0.047878,(Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.045666):0.730063,Lottia_gigantea_tyr1:0.154743):0.156381,(Lottia_gigantea_tyr2:0.709457,(Pinctada_fucata_tyr1:0.394589,(Pinctada_fucata_tyr4:0.271352,(Pinctada_fucata_tyr2:6.0E-6,Pinctada_fucata_tyr3:0.045355):0.255761):0.365785):0.179793):0.212697):0.408679):0.063093,Brugia_malayi_TYR3:0.292713):0.219597,Caenorhabditis_remanei_TYR5:0.704736):0.206275,(Nitrosomonas_europeae_tyr:0.74561,(Streptomyces_venezuelae_tyr:0.096353,Streptomyces_tsukubaensis_tyr:0.398716):0.208169):0.129481):0.1982,((Bacillus_megaterium_tyr1:1.0E-6,Bacillus_megaterium_tyr2:0.009295):0.288008,Polysphondylium_pallidum_tyr1:0.563308):0.110257):0.170366,((((Glycine_max_CO5:0.307389,(Glycine_max_CO7:1.0E-6,Glycine_max_CO6:0.010749):0.249276):0.110091,(((((((Glycine_max_CO11:0.0,Glycine_max_CO12:0.037921):0.011803,Glycine_max_CO9:0.090071):0.011449,Glycine_max_CO8:0.138045):0.054578,Glycine_max_CO10:0.058978):0.031134,Oryza_sativa_CO:0.21077):0.077368,((Glycine_max_CO4:0.016447,Glycine_max_CO3:0.040961):0.115418,Vitis_vinifera_CO:0.155967):0.104085):0.077134,(Glycine_max_CO1:1.0E-6,Glycine_max_CO2:0.018471):0.133243):8.0E-6):1.490137,(((Nematostella_vectensis_tyr3:0.298721,Nematostella_vectensis_tyr4:0.391307):0.222554,(Nematostella_vectensis_tyr2:0.774546,Hydra_magnipapillata_tyr:0.64196):0.295109):4.0E-6,Nematostella_vectensis_tyr1:1.048891):0.802588):0.331292,((Dictyostelium_discoideum_tyr2:0.01632,Dictyostelium_discoideum_tyr1:0.0):0.818975,Candidatus_nitrosopumilus_tyr:0.470771):3.2E-5):0.120355):0.032158,Phragmatopoma_californica_tyr:0.687141):0.179052,(((((Ectocarpus_siliculosus_tyr11:4.0E-6,Ectocarpus_siliculosus_tyr10:0.198059):0.064642,Ectocarpus_siliculosus_tyr9:0.076618):0.008647,Ectocarpus_siliculosus_tyr7:0.416743):0.114297,Ectocarpus_siliculosus_tyr8:0.080365):0.170776,(((Ectocarpus_siliculosus_tyr14:0.062946,(((Ectocarpus_siliculosus_tyr17:0.071354,Ectocarpus_siliculosus_tyr18:0.100289):0.038778,Ectocarpus_siliculosus_tyr16:0.037832):0.105313,Ectocarpus_siliculosus_tyr15:0.209424):0.168799):0.628112,(Ectocarpus_siliculosus_tyr12:0.092436,Ectocarpus_siliculosus_tyr13:1.0E-6):0.243751):0.250186,(((Ectocarpus_siliculosus_tyr5:0.365301,Ectocarpus_siliculosus_tyr6:0.164409):0.384723,Ectocarpus_siliculosus_tyr4:0.256332):0.073867,((Ectocarpus_siliculosus_tyr2:0.029109,Ectocarpus_siliculosus_tyr3:0.083076):0.165388,Ectocarpus_siliculosus_tyr1:0.247699):0.032338):0.693802):0.266761):0.842039):0.490816,(((Sepia_officinalis_Hc:0.124151,((Megathura_crenulata_Hc:0.262802,Aplysia_californica_Hc:0.112836):0.118218,Nucula_nucleus_Hc:0.206377):0.070973):0.787801,((((Ciona_intestinalis_HcC:0.203258,Ciona_intestinalis_HcD:4.0E-6):0.069785,Ciona_intestinalis_HcB:0.051054):0.067669,Ciona_intestinalis_HcA:0.121823):0.143403,(((Ciona_intestinalis_HcF:0.145019,Ciona_intestinalis_HcE:0.005118):0.156916,Ciona_intestinalis_HcI:0.163694):0.053086,(Ciona_intestinalis_HcH:0.068488,Ciona_intestinalis_HcG:0.286407):0.112936):0.33911):0.526107):0.275581,Lottia_gigantea_Hc:0.836562):0.324891):0.520693,Agaricus_bisporus_tyr:0.501579):0.145547,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.0):0.676677):0.204247,Aspergillus_aculeatus_tyr:0.615783):0.098195,(Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.009112):0.638424):0.685756,Neurospora_tetrasperma_tyr2:0.008642,Neurospora_crassa_tyr2:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61725] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE ML_tree = [&R] ((((Bacillus_megaterium_tyr2:0.01015,Bacillus_megaterium_tyr1:1.0E-6):0.389372,(Nitrosomonas_europeae_tyr:0.732847,Polysphondylium_pallidum_tyr1:0.637634):0.138331):0.21393,((Streptomyces_tsukubaensis_tyr:0.425232,Streptomyces_venezuelae_tyr:0.138918):0.361557,(Candidatus_nitrosopumilus_tyr:0.690588,(Dictyostelium_discoideum_tyr2:0.018798,Dictyostelium_discoideum_tyr1:2.0E-5):0.662368):0.125688):0.107601):0.0356215,(((Lottia_gigantea_Hc:0.879534,((Sepia_officinalis_Hc:0.225664,(Nucula_nucleus_Hc:0.241096,(Megathura_crenulata_Hc:0.31007,Aplysia_californica_Hc:0.167427):0.071404):0.047111):0.577993,((Ciona_intestinalis_HcA:0.115702,(Ciona_intestinalis_HcB:0.111369,(Ciona_intestinalis_HcD:0.028037,Ciona_intestinalis_HcC:0.121713):0.114857):0.09507):0.197257,((Ciona_intestinalis_HcF:0.104995,Ciona_intestinalis_HcE:0.034155):0.083435,(Ciona_intestinalis_HcG:0.212251,(Ciona_intestinalis_HcH:0.053341,Ciona_intestinalis_HcI:0.118667):0.107292):0.062482):0.251607):0.535834):0.330119):0.251334,((Aspergillus_aculeatus_tyr:0.610168,((Agaricus_bisporus_tyr:0.61919,(Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.010273):0.708977):0.132297,((Neurospora_crassa_tyr3:1.0E-6,Neurospora_tetrasperma_tyr3:0.009816):0.505363,(Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.019959):0.526718):0.138656):0.160111):0.270621,((Glycine_max_CO2:0.009818,Glycine_max_CO1:1.0E-6):0.035166,((Vitis_vinifera_CO:0.232459,((Glycine_max_CO4:0.036897,Glycine_max_CO3:0.051071):0.25082,(Glycine_max_CO5:0.225527,(Glycine_max_CO7:0.011152,Glycine_max_CO6:0.023007):0.255183):0.105622):0.033712):0.024832,(Oryza_sativa_CO:0.21329,(Glycine_max_CO8:0.128079,(Glycine_max_CO9:0.048807,(Glycine_max_CO10:0.1585,(Glycine_max_CO12:0.051374,Glycine_max_CO11:1.0E-6):0.020743):0.063259):0.081898):0.066818):0.053752):0.206834):1.53489):0.39384):0.584513,((((Ectocarpus_siliculosus_tyr4:0.295128,(Ectocarpus_siliculosus_tyr6:0.258094,Ectocarpus_siliculosus_tyr5:0.28478):0.368108):0.057972,(Ectocarpus_siliculosus_tyr1:0.2235,(Ectocarpus_siliculosus_tyr3:0.108262,Ectocarpus_siliculosus_tyr2:0.067256):0.171537):0.085349):0.578695,((Ectocarpus_siliculosus_tyr7:0.305503,(Ectocarpus_siliculosus_tyr8:0.187652,(Ectocarpus_siliculosus_tyr9:0.052064,(Ectocarpus_siliculosus_tyr11:0.026066,Ectocarpus_siliculosus_tyr10:0.178651):0.072162):0.044579):0.209566):0.461972,((Ectocarpus_siliculosus_tyr12:0.168102,Ectocarpus_siliculosus_tyr13:2.0E-6):0.368002,(Ectocarpus_siliculosus_tyr14:0.090051,(Ectocarpus_siliculosus_tyr15:0.253141,(Ectocarpus_siliculosus_tyr16:0.064871,(Ectocarpus_siliculosus_tyr18:0.1409,Ectocarpus_siliculosus_tyr17:0.090809):0.033798):0.088663):0.170417):0.403924):0.306472):0.12426):1.172959,((Nematostella_vectensis_tyr1:0.839335,((Nematostella_vectensis_tyr4:0.408163,Nematostella_vectensis_tyr3:0.396192):0.221518,(Nematostella_vectensis_tyr2:0.965652,Hydra_magnipapillata_tyr:0.792227):0.267615):0.09288):1.05773,(Phragmatopoma_californica_tyr:0.616946,(((Lottia_gigantea_tyr1:0.338002,(Sepia_officinalis_tyr:0.07146,(Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.045203):0.670794):0.239494,(Lottia_gigantea_tyr2:0.831728,(Pinctada_fucata_tyr1:0.621465,(Pinctada_fucata_tyr4:0.179296,(Pinctada_fucata_tyr2:3.0E-6,Pinctada_fucata_tyr3:0.019557):0.227917):0.416124):0.186431):0.196291):0.271676,(Caenorhabditis_remanei_TYR5:0.843909,(Brugia_malayi_TYR1:0.183181,(((Caenorhabditis_elegans_TYR3:0.020471,(Caenorhabditis_briggsae_TYR3:1.0E-6,Caenorhabditis_remanei_TYR3:0.049165):0.008194):0.203849,((Caenorhabditis_briggsae_TYR6:5.0E-6,Caenorhabditis_elegans_TYR5:0.041012):1.059664,(Caenorhabditis_briggsae_TYR4:2.0E-6,(Caenorhabditis_remanei_TYR4:0.009056,Caenorhabditis_elgans_TYR4:0.019115):0.047444):1.4E-5):0.117987):0.156789,(Brugia_malayi_TYR2:0.365072,(Brugia_malayi_TYR3:0.299453,((Brugia_malayi_TYR4:0.24142,(Caenorhabditis_elegans_TYR2:1.0E-6,(Caenorhabditis_briggsae_TYR2:0.032436,Caenorhabditis_remanei_TYR2:0.008753):0.021013):0.096872):0.111573,(Caenorhabditis_elegans_TYR1:0.0,(Caenorhabditis_remanei_TYR1:0.010282,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.02765):0.018551):0.170794):0.136182):0.041514):0.066206):0.023381):0.249037):0.170198):0.045118):0.112421):0.057387):0.086032):0.0356215); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61696] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_26 = [&R] ((((((((((((((((((((((Caenorhabditis_remanei_TYR2:0.008262,Caenorhabditis_briggsae_TYR2:0.008709):0.004675,(((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.016351,Caenorhabditis_remanei_TYR1:0.016609):0.016798,Caenorhabditis_elegans_TYR1:0.0):0.15768):0.021853,Caenorhabditis_elegans_TYR2:1.0E-6):0.114681,Brugia_malayi_TYR4:0.106256):0.201107,Brugia_malayi_TYR3:0.261357):0.010622,Brugia_malayi_TYR2:0.243932):0.046777,Brugia_malayi_TYR1:0.059677):4.0E-6,(((((Caenorhabditis_elgans_TYR4:0.034053,Caenorhabditis_remanei_TYR4:0.0):0.041615,Caenorhabditis_briggsae_TYR4:2.0E-6):3.0E-6,(Caenorhabditis_elegans_TYR5:0.0,Caenorhabditis_briggsae_TYR6:0.0):0.919287):0.054135,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_elegans_TYR3:0.0):0.013001,Caenorhabditis_remanei_TYR3:0.06918):0.210545):0.070841,Caenorhabditis_remanei_TYR5:0.519377):0.13657):0.222932,((((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.034569,Sepia_officinalis_tyr:0.036441):0.436698,Lottia_gigantea_tyr1:0.200688):0.229775,(((Pinctada_fucata_tyr1:0.507837,((Pinctada_fucata_tyr3:1.0E-6,Pinctada_fucata_tyr2:0.008606):0.151514,Pinctada_fucata_tyr4:0.167472):0.351881):0.049708,Lottia_gigantea_tyr2:0.620265):0.244669,Phragmatopoma_californica_tyr:0.53618):0.110825):0.134401):0.168709,((((((Ectocarpus_siliculosus_tyr11:0.00311,Ectocarpus_siliculosus_tyr10:0.176674):0.061169,Ectocarpus_siliculosus_tyr9:0.017217):0.024286,Ectocarpus_siliculosus_tyr8:0.220268):0.150844,Ectocarpus_siliculosus_tyr7:0.296094):0.458705,(((((Ectocarpus_siliculosus_tyr17:0.070916,Ectocarpus_siliculosus_tyr15:0.196699):0.0557,Ectocarpus_siliculosus_tyr16:0.029036):0.025286,Ectocarpus_siliculosus_tyr18:0.079627):0.151724,Ectocarpus_siliculosus_tyr14:0.016844):0.228489,(Ectocarpus_siliculosus_tyr12:0.208363,Ectocarpus_siliculosus_tyr13:2.0E-6):0.407982):0.244358):0.046965,((Ectocarpus_siliculosus_tyr5:0.19471,Ectocarpus_siliculosus_tyr6:0.188575):0.187708,((Ectocarpus_siliculosus_tyr1:0.293277,(Ectocarpus_siliculosus_tyr3:0.072649,Ectocarpus_siliculosus_tyr2:0.097501):0.200277):0.057428,Ectocarpus_siliculosus_tyr4:0.242162):0.129409):0.327406):0.79502):0.219997,((Nematostella_vectensis_tyr1:0.664074,Nematostella_vectensis_tyr3:0.289009):0.046733,((Nematostella_vectensis_tyr2:0.972346,Hydra_magnipapillata_tyr:0.453817):0.25359,Nematostella_vectensis_tyr4:0.161854):0.099489):0.683984):0.143786,(((Dictyostelium_discoideum_tyr2:1.0E-6,Dictyostelium_discoideum_tyr1:0.008642):0.431238,(Streptomyces_tsukubaensis_tyr:0.153207,Streptomyces_venezuelae_tyr:0.148402):0.270886):0.078058,(((Nitrosomonas_europeae_tyr:0.553761,Polysphondylium_pallidum_tyr1:0.613611):0.150122,(Bacillus_megaterium_tyr1:1.0E-6,Bacillus_megaterium_tyr2:0.017519):0.335894):0.02726,Candidatus_nitrosopumilus_tyr:0.39394):0.129723):0.110355):0.54847,(((((Ciona_intestinalis_HcH:0.0,Ciona_intestinalis_HcI:0.065394):0.040113,Ciona_intestinalis_HcG:0.175937):0.071696,(Ciona_intestinalis_HcF:0.107844,Ciona_intestinalis_HcE:0.004965):0.101479):0.152882,((Ciona_intestinalis_HcC:0.086621,Ciona_intestinalis_HcB:0.022811):0.045121,Ciona_intestinalis_HcD:2.0E-6):0.468606):0.392512,(Aplysia_californica_Hc:0.127008,(Megathura_crenulata_Hc:0.13496,(Sepia_officinalis_Hc:0.19133,Nucula_nucleus_Hc:0.215473):0.073312):0.119559):0.428769):0.490199):0.177845,(Ciona_intestinalis_HcA:0.745088,Lottia_gigantea_Hc:1.3E-5):0.861108):0.180717,Aspergillus_aculeatus_tyr:0.437699):0.224046,((Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.008567):0.438266,(Neurospora_tetrasperma_tyr3:0.018029,Neurospora_crassa_tyr3:1.0E-6):0.338333):0.229303):0.116569,Agaricus_bisporus_tyr:0.337134):0.090623,(Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0):0.561275):1.534644,(Glycine_max_CO1:1.0E-6,Glycine_max_CO2:0.01774):4.0E-6):0.215825,(((Glycine_max_CO9:0.052074,(Glycine_max_CO11:1.0E-6,(Glycine_max_CO10:0.161924,Glycine_max_CO12:0.052573):0.015462):0.059612):0.076594,Glycine_max_CO8:0.101093):0.052731,(Oryza_sativa_CO:0.166327,Vitis_vinifera_CO:0.187729):0.01423):1.4E-5):0.043653,(Glycine_max_CO5:0.180543,(Glycine_max_CO6:0.031544,Glycine_max_CO7:0.021573):0.207336):0.049346):0.301375,Glycine_max_CO4:0.018542,Glycine_max_CO3:0.019739); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61722] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_2 = [&R] (((((((((((((((((((Caenorhabditis_briggsae_TYR4:0.0,(Caenorhabditis_elgans_TYR4:0.028037,(((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.058162):0.008931,Caenorhabditis_elegans_TYR3:0.009715):0.281285,Caenorhabditis_remanei_TYR4:0.0):0.027207):0.075291):0.139476,(Caenorhabditis_elegans_TYR5:0.043409,Caenorhabditis_briggsae_TYR6:0.013356):0.968052):0.089191,Brugia_malayi_TYR1:0.164761):0.045459,(((((Caenorhabditis_elegans_TYR2:0.0,(Caenorhabditis_remanei_TYR2:0.009021,Caenorhabditis_briggsae_TYR2:0.031726):0.010299):0.13094,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.018003,Caenorhabditis_remanei_TYR1:0.0):0.027295,Caenorhabditis_elegans_TYR1:0.0):0.205191):0.029002,Brugia_malayi_TYR4:0.139757):0.052195,Brugia_malayi_TYR3:0.380178):0.084018,Brugia_malayi_TYR2:0.29573):0.065343):0.254843,(((((Ectocarpus_siliculosus_tyr15:0.048256,(((Ectocarpus_siliculosus_tyr17:0.096516,Ectocarpus_siliculosus_tyr18:0.076072):0.051816,Ectocarpus_siliculosus_tyr16:0.074643):0.108208,Ectocarpus_siliculosus_tyr14:0.219111):0.286716):0.431269,(Ectocarpus_siliculosus_tyr12:0.198463,Ectocarpus_siliculosus_tyr13:5.0E-6):0.32299):0.482142,(((Ectocarpus_siliculosus_tyr9:0.069979,Ectocarpus_siliculosus_tyr11:0.053203):0.041235,(Ectocarpus_siliculosus_tyr10:0.161348,Ectocarpus_siliculosus_tyr8:0.114634):0.028236):0.133399,Ectocarpus_siliculosus_tyr7:0.310959):0.20682):0.138441,((((Ectocarpus_siliculosus_tyr3:0.099476,Ectocarpus_siliculosus_tyr2:0.05329):0.143141,Ectocarpus_siliculosus_tyr1:0.237788):0.100614,Ectocarpus_siliculosus_tyr4:0.270023):0.139522,(Ectocarpus_siliculosus_tyr5:0.348619,Ectocarpus_siliculosus_tyr6:0.229794):0.416467):0.544513):0.982417,((((Pinctada_fucata_tyr1:0.878342,(Pinctada_fucata_tyr4:0.267798,(Pinctada_fucata_tyr3:1.0E-6,Pinctada_fucata_tyr2:0.019415):0.285041):0.351618):0.206537,Phragmatopoma_californica_tyr:0.654475):0.11382,Lottia_gigantea_tyr2:1.091631):0.178881,((((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.110247,Sepia_officinalis_tyr:0.091273):0.813748,Caenorhabditis_remanei_TYR5:0.867299):0.011645,Lottia_gigantea_tyr1:0.399492):0.22367):0.163975):0.134536):0.160319,(((((Nematostella_vectensis_tyr4:0.546439,(Nematostella_vectensis_tyr1:1.080258,Nematostella_vectensis_tyr3:0.239576):0.055632):1.0E-5,(Nematostella_vectensis_tyr2:1.045759,Hydra_magnipapillata_tyr:0.72946):0.45062):0.755799,(Streptomyces_venezuelae_tyr:0.084887,Streptomyces_tsukubaensis_tyr:0.564134):0.253826):0.165423,(Dictyostelium_discoideum_tyr2:0.009041,Dictyostelium_discoideum_tyr1:0.0):0.783504):0.184729,(((Polysphondylium_pallidum_tyr1:0.377923,Nitrosomonas_europeae_tyr:0.673662):0.185514,(Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.335807):0.230172,Candidatus_nitrosopumilus_tyr:0.689788):0.207172):0.019324):0.572522,((Glycine_max_CO1:0.0,Glycine_max_CO2:0.0):0.112282,((((Glycine_max_CO8:0.17288,Glycine_max_CO9:0.062787):0.036504,((Glycine_max_CO11:0.008953,Glycine_max_CO12:0.039911):0.0437,((Glycine_max_CO7:0.0,Glycine_max_CO6:0.010078):0.247274,(Glycine_max_CO10:0.110461,Oryza_sativa_CO:0.254864):0.07362):0.02718):0.068078):0.07564,(Vitis_vinifera_CO:0.114666,(Glycine_max_CO4:0.029705,Glycine_max_CO3:0.067564):0.320499):0.075253):0.141381,Glycine_max_CO5:0.25127):0.02629):1.431684):0.557683,(((Nucula_nucleus_Hc:0.339797,Sepia_officinalis_Hc:0.132362):0.152746,Megathura_crenulata_Hc:0.44027):0.032684,Aplysia_californica_Hc:0.112843):0.689973):0.660857,(Ciona_intestinalis_HcH:0.024199,Ciona_intestinalis_HcI:0.157328):0.091483):0.091733,Ciona_intestinalis_HcG:0.224022):0.023083,(Ciona_intestinalis_HcE:8.0E-6,Ciona_intestinalis_HcF:0.073303):0.11184):0.29838,Ciona_intestinalis_HcA:4.0E-6):0.090286,((Ciona_intestinalis_HcC:0.093001,Ciona_intestinalis_HcD:0.0):0.119545,Ciona_intestinalis_HcB:0.131067):0.148274):1.038068,Lottia_gigantea_Hc:0.899107):0.914654,Agaricus_bisporus_tyr:0.403576):0.276026,(Neurospora_tetrasperma_tyr3:0.01824,Neurospora_crassa_tyr3:1.0E-6):0.52286):0.21173,(Neurospora_tetrasperma_tyr2:0.009871,Neurospora_crassa_tyr2:0.0):0.396763):0.128289,Aspergillus_aculeatus_tyr:0.620018):0.745769,Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.030498); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61698] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_22 = [&R] (((Glycine_max_CO12:0.038798,((((((((((((((((Brugia_malayi_TYR3:0.258268,(((Nitrosomonas_europeae_tyr:0.528804,(((Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.373241,Candidatus_nitrosopumilus_tyr:0.555493):0.016465,((Dictyostelium_discoideum_tyr2:0.019069,Dictyostelium_discoideum_tyr1:0.017016):0.575884,(Streptomyces_venezuelae_tyr:0.226901,Streptomyces_tsukubaensis_tyr:0.249852):0.162939):0.135447):0.201492):0.176168,Caenorhabditis_remanei_TYR5:0.512386):0.185198,Polysphondylium_pallidum_tyr1:0.711832):0.089859):0.154486,(((((Caenorhabditis_remanei_TYR3:0.052742,Caenorhabditis_briggsae_TYR3:1.0E-6):0.008046,Caenorhabditis_elegans_TYR3:0.012028):0.213504,((Caenorhabditis_remanei_TYR4:0.009458,Caenorhabditis_elgans_TYR4:1.0E-6):0.028558,Caenorhabditis_briggsae_TYR4:0.0):0.073603):0.164312,(Caenorhabditis_elegans_TYR5:0.010936,Caenorhabditis_briggsae_TYR6:0.057737):0.523529):0.037588,Brugia_malayi_TYR1:0.248553):0.037344):0.037181,(((((Caenorhabditis_remanei_TYR2:0.0,Caenorhabditis_elegans_TYR2:0.0):0.009909,Caenorhabditis_briggsae_TYR2:0.045321):0.045682,((Caenorhabditis_remanei_TYR1:1.0E-6,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.018569):0.018386,Caenorhabditis_elegans_TYR1:0.0):0.171297):0.064276,Brugia_malayi_TYR4:0.132638):0.062556,Brugia_malayi_TYR2:0.289886):2.0E-6):0.143942,(((Nematostella_vectensis_tyr3:0.244766,Nematostella_vectensis_tyr4:0.407038):0.067639,(Nematostella_vectensis_tyr2:0.696283,Hydra_magnipapillata_tyr:0.467394):0.493351):0.082226,Nematostella_vectensis_tyr1:0.535375):0.664838):0.237643,((((Ciona_intestinalis_HcD:0.059935,(Ciona_intestinalis_HcA:1.6E-5,(((Ciona_intestinalis_HcF:0.054929,Ciona_intestinalis_HcE:0.008183):0.063581,(Ciona_intestinalis_HcI:0.050429,Ciona_intestinalis_HcH:2.0E-6):0.095232):0.004574,Ciona_intestinalis_HcG:0.240413):0.450891):0.055132):0.076801,(Ciona_intestinalis_HcC:0.027719,Ciona_intestinalis_HcB:0.034128):0.009346):0.806327,(Sepia_officinalis_Hc:0.191019,(Nucula_nucleus_Hc:0.3163,(Aplysia_californica_Hc:0.199057,Megathura_crenulata_Hc:0.23042):0.04898):0.029226):0.349336):0.153658,((((Neurospora_tetrasperma_tyr1:0.0,Neurospora_crassa_tyr1:0.0):0.619322,Agaricus_bisporus_tyr:0.385965):0.141553,(((Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.020939):0.184317,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.020604):0.417363):0.277538,Aspergillus_aculeatus_tyr:0.419907):0.066704):0.541758,Lottia_gigantea_Hc:0.795894):0.24409):0.605083):0.065908,(Sepia_officinalis_tyr:0.093265,(Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):2.0E-6):0.535838):0.02091,(Phragmatopoma_californica_tyr:0.792441,Lottia_gigantea_tyr1:0.170863):0.323431):0.113652,((((Pinctada_fucata_tyr3:0.010103,Pinctada_fucata_tyr2:1.0E-6):0.100737,Pinctada_fucata_tyr4:0.198897):0.395684,((((Ectocarpus_siliculosus_tyr13:2.0E-6,Ectocarpus_siliculosus_tyr12:0.128464):0.507243,((Ectocarpus_siliculosus_tyr16:0.008538,((Ectocarpus_siliculosus_tyr14:0.228341,Ectocarpus_siliculosus_tyr18:0.020703):0.054198,Ectocarpus_siliculosus_tyr17:0.047678):0.033966):0.087408,Ectocarpus_siliculosus_tyr15:0.156383):0.474576):0.071431,(((Ectocarpus_siliculosus_tyr6:0.249768,Ectocarpus_siliculosus_tyr5:0.193248):0.311699,Ectocarpus_siliculosus_tyr4:0.163692):0.150716,(Ectocarpus_siliculosus_tyr1:0.076146,(Ectocarpus_siliculosus_tyr2:0.063775,Ectocarpus_siliculosus_tyr3:0.139173):0.13287):0.089863):0.388089):0.162196,(Ectocarpus_siliculosus_tyr7:0.227053,((Ectocarpus_siliculosus_tyr8:0.168722,(Ectocarpus_siliculosus_tyr9:1.0E-6,Ectocarpus_siliculosus_tyr11:0.059786):0.016687):0.093708,Ectocarpus_siliculosus_tyr10:0.104121):0.151223):0.28872):0.672765):0.237262,(Pinctada_fucata_tyr1:0.407258,Lottia_gigantea_tyr2:0.721797):0.065913):0.044761):1.717987,Vitis_vinifera_CO:0.22082):6.0E-6,Glycine_max_CO5:0.233388):0.061376,(Glycine_max_CO1:0.0,Glycine_max_CO2:0.020216):0.106583):0.059247,Oryza_sativa_CO:0.288636):0.057012,Glycine_max_CO8:0.129343):0.088106,Glycine_max_CO9:0.064252):0.109796,Glycine_max_CO10:0.143821):0.035897,Glycine_max_CO11:1.0E-6):0.024678):0.097571,(Glycine_max_CO3:0.0,Glycine_max_CO4:0.0):0.274476):0.216102,Glycine_max_CO7:0.010908,Glycine_max_CO6:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61718] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_19 = [&R] ((((((((((((((((((Caenorhabditis_remanei_TYR3:0.042546,Caenorhabditis_briggsae_TYR3:0.0):0.006682,Caenorhabditis_elegans_TYR3:0.035325):0.089591,(Caenorhabditis_remanei_TYR4:0.0,(Caenorhabditis_elgans_TYR4:0.008188,Caenorhabditis_briggsae_TYR4:0.016219):0.016194):0.13442):0.185155,((Brugia_malayi_TYR3:0.220333,((Brugia_malayi_TYR4:0.266533,(Caenorhabditis_briggsae_TYR2:0.037428,(Caenorhabditis_elegans_TYR2:0.008832,Caenorhabditis_remanei_TYR2:0.0):0.013128):0.062588):0.119428,((Caenorhabditis_remanei_TYR1:0.009937,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.02354):0.024808,Caenorhabditis_elegans_TYR1:0.0):0.089512):0.096637):0.05576,Brugia_malayi_TYR2:0.452497):0.045313):0.020986,(Brugia_malayi_TYR1:0.177009,(Caenorhabditis_briggsae_TYR6:1.0E-6,Caenorhabditis_elegans_TYR5:0.047528):1.011749):0.098558):0.334678,Caenorhabditis_remanei_TYR5:0.830954):0.279611,(Streptomyces_venezuelae_tyr:1.6E-5,Streptomyces_tsukubaensis_tyr:0.712009):0.490291):0.059394,((Nitrosomonas_europeae_tyr:0.749196,Polysphondylium_pallidum_tyr1:0.47831):0.226677,(Bacillus_megaterium_tyr2:0.0092,Bacillus_megaterium_tyr1:2.0E-6):0.481309):0.217212):0.202303,((Phragmatopoma_californica_tyr:0.557983,(((Pinctada_fucata_tyr3:0.031597,Pinctada_fucata_tyr2:0.003313):0.295226,Pinctada_fucata_tyr4:0.12682):0.427963,((Lottia_gigantea_tyr2:0.674545,Lottia_gigantea_Hc:1.027336):0.14642,Pinctada_fucata_tyr1:0.419535):0.084498):0.200371):0.043678,((((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):2.0E-6,Sepia_officinalis_tyr:0.07793):0.356722,Lottia_gigantea_tyr1:0.332496):0.127502,((Nematostella_vectensis_tyr1:0.74079,Nematostella_vectensis_tyr2:1.051628):0.114917,((Hydra_magnipapillata_tyr:0.812092,Nematostella_vectensis_tyr3:0.177901):0.295387,Nematostella_vectensis_tyr4:0.516525):0.274647):1.173534):0.183879):0.141815):1.0E-6,(Candidatus_nitrosopumilus_tyr:0.700889,(Dictyostelium_discoideum_tyr1:1.0E-6,Dictyostelium_discoideum_tyr2:0.026014):0.546481):0.165681):0.282262,(((Ciona_intestinalis_HcF:0.094369,Ciona_intestinalis_HcE:0.091886):0.272062,((Ciona_intestinalis_HcI:0.283723,Ciona_intestinalis_HcH:2.0E-6):0.20751,Ciona_intestinalis_HcG:0.206725):0.241616):0.211138,(((Ciona_intestinalis_HcC:0.19688,Ciona_intestinalis_HcD:1.0E-6):0.149088,Ciona_intestinalis_HcB:0.133801):0.063283,Ciona_intestinalis_HcA:0.281056):0.107858):0.953026):0.139123,((Ectocarpus_siliculosus_tyr14:0.064121,((Ectocarpus_siliculosus_tyr16:0.144129,(Ectocarpus_siliculosus_tyr18:0.14422,Ectocarpus_siliculosus_tyr17:0.011051):0.055034):0.049647,Ectocarpus_siliculosus_tyr15:0.267717):0.126251):0.254925,((((((Ectocarpus_siliculosus_tyr6:0.251949,Ectocarpus_siliculosus_tyr5:0.285168):0.407442,Ectocarpus_siliculosus_tyr4:0.4544):0.129121,Ectocarpus_siliculosus_tyr1:0.264603):0.083354,(Ectocarpus_siliculosus_tyr3:0.102517,Ectocarpus_siliculosus_tyr2:0.08534):0.040515):0.684327,(Ectocarpus_siliculosus_tyr7:0.355538,((Ectocarpus_siliculosus_tyr9:0.033821,(Ectocarpus_siliculosus_tyr11:0.021124,Ectocarpus_siliculosus_tyr10:0.122319):0.050242):0.068569,Ectocarpus_siliculosus_tyr8:0.13068):0.119797):0.317065):0.262865,(Ectocarpus_siliculosus_tyr12:0.134957,Ectocarpus_siliculosus_tyr13:0.0):0.236665):0.310589):1.050972):0.241223,(Sepia_officinalis_Hc:0.103696,((Nucula_nucleus_Hc:0.218858,Aplysia_californica_Hc:0.154409):0.069404,Megathura_crenulata_Hc:0.2942):0.125024):0.825351):0.490251,(((((Glycine_max_CO7:0.0,Glycine_max_CO6:0.010144):0.197139,Glycine_max_CO5:0.196008):0.137192,(((Glycine_max_CO9:0.041456,((Glycine_max_CO11:0.0,Glycine_max_CO12:0.054536):0.018131,Glycine_max_CO10:0.078491):0.062128):0.03723,Glycine_max_CO8:0.05449):0.034718,Oryza_sativa_CO:0.108268):0.056367):0.021805,((Glycine_max_CO3:0.04255,Glycine_max_CO4:0.002688):0.146245,Vitis_vinifera_CO:0.169097):0.065206):0.178982,(Glycine_max_CO2:0.0,Glycine_max_CO1:0.0):5.0E-6):1.195483):0.264643,((Neurospora_tetrasperma_tyr3:0.007962,Neurospora_crassa_tyr3:0.0):0.686307,Agaricus_bisporus_tyr:0.539109):2.4E-5):0.205664,(Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.00809):0.534471):0.069095,Aspergillus_aculeatus_tyr:0.693963):0.755429,Neurospora_tetrasperma_tyr1:0.0,Neurospora_crassa_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61715] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_5 = [&R] (((((((((((((((Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_remanei_TYR4:0.016814,Caenorhabditis_elgans_TYR4:0.026244):0.03456):0.063975,((Caenorhabditis_remanei_TYR3:0.017147,Caenorhabditis_briggsae_TYR3:0.0):0.008475,Caenorhabditis_elegans_TYR3:0.008668):0.204625):0.104045,(((Caenorhabditis_elegans_TYR5:0.036712,Caenorhabditis_briggsae_TYR6:3.0E-6):0.823583,Brugia_malayi_TYR2:0.195397):0.047106,((Brugia_malayi_TYR4:0.174792,(((Caenorhabditis_elegans_TYR1:0.015422,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.049608):0.026346,Caenorhabditis_remanei_TYR1:1.0E-6):0.294797,(Caenorhabditis_elegans_TYR2:1.0E-6,(Caenorhabditis_briggsae_TYR2:0.017452,Caenorhabditis_remanei_TYR2:1.0E-6):0.03435):0.124537):0.063628):0.117995,Brugia_malayi_TYR1:0.186865):0.050841):0.03428):0.042242,Brugia_malayi_TYR3:0.317439):0.393309,((Polysphondylium_pallidum_tyr1:0.702618,Nitrosomonas_europeae_tyr:0.602257):0.110052,((Streptomyces_venezuelae_tyr:0.248492,Streptomyces_tsukubaensis_tyr:0.303069):0.262032,(Candidatus_nitrosopumilus_tyr:0.58175,(Bacillus_megaterium_tyr2:0.008965,Bacillus_megaterium_tyr1:1.0E-6):0.251594):0.04953):0.129923):0.089444):0.128068,(((Dictyostelium_discoideum_tyr1:0.019402,Dictyostelium_discoideum_tyr2:0.013559):0.470023,Phragmatopoma_californica_tyr:0.263825):0.082296,(((Nematostella_vectensis_tyr3:0.33555,(Nematostella_vectensis_tyr1:0.719137,(Hydra_magnipapillata_tyr:0.832781,Nematostella_vectensis_tyr2:0.78541):0.389884):0.231831):0.198588,Nematostella_vectensis_tyr4:0.137623):0.939611,Caenorhabditis_remanei_TYR5:0.567488):0.186244):0.100553):0.117787,(((Ectocarpus_siliculosus_tyr7:0.278616,(Ectocarpus_siliculosus_tyr10:0.089983,(Ectocarpus_siliculosus_tyr11:0.001296,(Ectocarpus_siliculosus_tyr8:0.190277,Ectocarpus_siliculosus_tyr9:0.039861):0.159482):0.095478):0.210082):0.47097,(((((Ectocarpus_siliculosus_tyr17:0.047966,Ectocarpus_siliculosus_tyr18:0.10786):0.039404,Ectocarpus_siliculosus_tyr16:0.078051):0.064754,Ectocarpus_siliculosus_tyr15:0.267507):0.111559,Ectocarpus_siliculosus_tyr14:0.078132):0.478221,(Ectocarpus_siliculosus_tyr13:2.0E-6,Ectocarpus_siliculosus_tyr12:0.129363):0.256515):0.362393):0.143919,((((Ectocarpus_siliculosus_tyr2:0.039704,Ectocarpus_siliculosus_tyr3:0.069834):0.198361,Ectocarpus_siliculosus_tyr1:0.215431):0.017434,Ectocarpus_siliculosus_tyr4:0.306708):0.076433,(Ectocarpus_siliculosus_tyr5:0.325306,Ectocarpus_siliculosus_tyr6:0.1846):0.22362):0.34378):0.618314):0.273816,((Pinctada_fucata_tyr1:0.406892,((Pinctada_fucata_tyr3:0.026081,Pinctada_fucata_tyr2:1.0E-6):0.240625,Pinctada_fucata_tyr4:0.150262):0.480071):0.204027,Lottia_gigantea_tyr2:0.519018):0.128393):0.053638,(((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.078534,Sepia_officinalis_tyr:0.070686):0.68047,Lottia_gigantea_tyr1:0.183323):0.39211):0.495455,(((Ciona_intestinalis_HcD:0.034636,(((Ciona_intestinalis_HcG:0.214377,(Ciona_intestinalis_HcH:0.119627,Ciona_intestinalis_HcI:0.153577):0.109865):0.086672,(Ciona_intestinalis_HcE:0.060721,Ciona_intestinalis_HcF:0.073213):0.073959):0.536044,(Ciona_intestinalis_HcB:0.034387,Ciona_intestinalis_HcC:7.0E-6):0.144483):1.0E-6):0.283148,Ciona_intestinalis_HcA:0.07183):0.334009,((Sepia_officinalis_Hc:0.158131,Megathura_crenulata_Hc:0.521456):0.115689,(Nucula_nucleus_Hc:0.196618,Aplysia_californica_Hc:0.235293):6.0E-6):0.717319):0.392772):0.13599,((((Glycine_max_CO1:0.0,Glycine_max_CO2:0.017579):0.194516,(((Oryza_sativa_CO:0.209906,Vitis_vinifera_CO:0.171146):0.028158,(Glycine_max_CO3:0.086202,Glycine_max_CO4:0.008761):0.192162):0.047402,(((Glycine_max_CO7:0.0,Glycine_max_CO6:0.043934):0.218429,(Glycine_max_CO10:0.038995,((Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.035206):0.017057,Glycine_max_CO9:0.089264):0.043052):0.03667):0.053706,Glycine_max_CO8:0.244759):0.149268):0.081034):0.076141,Glycine_max_CO5:0.129102):1.772983,Lottia_gigantea_Hc:0.297303):0.279761):0.57117,Agaricus_bisporus_tyr:0.838198):0.160721,(Neurospora_tetrasperma_tyr3:0.008765,Neurospora_crassa_tyr3:1.0E-6):0.382891):0.190536,(Aspergillus_aculeatus_tyr:0.839086,(Neurospora_tetrasperma_tyr2:0.026096,Neurospora_crassa_tyr2:0.0):0.339899):0.189875):0.777113,Neurospora_tetrasperma_tyr1:0.009652,Neurospora_crassa_tyr1:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61701] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_28 = [&R] (((((((((((((((((Ectocarpus_siliculosus_tyr10:0.081149,(Ectocarpus_siliculosus_tyr8:0.14652,(Ectocarpus_siliculosus_tyr11:0.070431,Ectocarpus_siliculosus_tyr9:1.0E-6):0.031199):0.080176):0.2733,Ectocarpus_siliculosus_tyr7:0.265449):0.25652,(((Ectocarpus_siliculosus_tyr5:0.224513,Ectocarpus_siliculosus_tyr6:0.196024):0.309761,(((Ectocarpus_siliculosus_tyr3:0.122146,Ectocarpus_siliculosus_tyr2:0.053511):0.11192,Ectocarpus_siliculosus_tyr1:0.240392):0.173015,Ectocarpus_siliculosus_tyr4:0.20265):0.092269):0.417186,((Ectocarpus_siliculosus_tyr13:2.0E-6,Ectocarpus_siliculosus_tyr12:0.134435):0.342509,((((Ectocarpus_siliculosus_tyr18:0.080664,Ectocarpus_siliculosus_tyr16:0.052288):1.0E-6,Ectocarpus_siliculosus_tyr17:0.116082):0.111855,Ectocarpus_siliculosus_tyr15:0.27997):0.112498,Ectocarpus_siliculosus_tyr14:0.035842):0.328938):0.263176):0.201183):0.396871,(((((Brugia_malayi_TYR3:0.405594,Brugia_malayi_TYR2:0.166634):0.066996,(((((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.055244,Caenorhabditis_remanei_TYR1:0.018433):0.026738,Caenorhabditis_elegans_TYR1:1.0E-6):0.24213,(Caenorhabditis_briggsae_TYR2:0.004879,(Caenorhabditis_remanei_TYR2:0.017312,Caenorhabditis_elegans_TYR2:0.019921):0.038618):0.059258):0.068919,Brugia_malayi_TYR4:0.115163):0.072306):0.16074,(((Caenorhabditis_elegans_TYR5:0.01765,Caenorhabditis_briggsae_TYR6:0.010612):0.822787,(Caenorhabditis_briggsae_TYR4:1.0E-6,(((Caenorhabditis_elegans_TYR3:0.018822,Caenorhabditis_briggsae_TYR3:0.0):5.0E-6,Caenorhabditis_remanei_TYR3:0.06978):0.318596,(Caenorhabditis_remanei_TYR4:0.0,Caenorhabditis_elgans_TYR4:0.0):0.019494):0.027249):0.220284):0.083808,Brugia_malayi_TYR1:0.21085):0.069615):0.264736,(((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):3.0E-6,Sepia_officinalis_tyr:0.140351):0.78262,Lottia_gigantea_tyr1:0.211788):0.270908):0.162296,Caenorhabditis_remanei_TYR5:0.528578):0.087787):0.112001,(Phragmatopoma_californica_tyr:0.600445,((Pinctada_fucata_tyr4:0.079671,(Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.008911):0.178007):0.65846,(Lottia_gigantea_tyr2:0.924539,Pinctada_fucata_tyr1:0.51003):0.132415):0.148366):0.057469):0.20133,(((Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.272699,Candidatus_nitrosopumilus_tyr:0.688475):0.138733,((Streptomyces_venezuelae_tyr:0.15552,Streptomyces_tsukubaensis_tyr:0.322809):0.138659,(Dictyostelium_discoideum_tyr2:0.0,Dictyostelium_discoideum_tyr1:0.008238):0.692963):0.129421):0.190353):0.025581,Nitrosomonas_europeae_tyr:0.661065):0.073626,(Polysphondylium_pallidum_tyr1:0.558006,(((Nematostella_vectensis_tyr2:1.19348,Hydra_magnipapillata_tyr:0.228562):0.294349,(Nematostella_vectensis_tyr4:0.156958,Nematostella_vectensis_tyr3:0.476812):0.225465):0.003717,Nematostella_vectensis_tyr1:0.641336):0.656176):0.083298):0.321061,(((((Glycine_max_CO6:0.007973,Glycine_max_CO7:0.011243):0.274779,((Glycine_max_CO1:0.0,Glycine_max_CO2:0.0):0.205137,Glycine_max_CO5:0.17203):0.113022):0.075318,(((((Glycine_max_CO10:0.19891,Glycine_max_CO12:0.018141):0.019427,Glycine_max_CO11:0.0):0.046806,Glycine_max_CO9:0.072555):0.068792,Glycine_max_CO8:0.104028):0.075782,(Oryza_sativa_CO:0.15124,Vitis_vinifera_CO:0.165235):0.057626):0.045854):0.150593,(Glycine_max_CO3:0.021048,Glycine_max_CO4:0.037134):0.091923):1.766406,(Agaricus_bisporus_tyr:0.699739,((((Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0):0.82147,(Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.018859):0.39686):0.24143,(Neurospora_tetrasperma_tyr3:0.019063,Neurospora_crassa_tyr3:1.0E-6):0.496529):0.26934,Aspergillus_aculeatus_tyr:0.464394):0.147948):0.343705):0.304712):0.452609,Lottia_gigantea_Hc:0.609661):0.303368,((Megathura_crenulata_Hc:0.413197,(Sepia_officinalis_Hc:0.234565,Nucula_nucleus_Hc:0.274265):0.06942):0.045391,Aplysia_californica_Hc:0.06476):0.296657):0.749787,(Ciona_intestinalis_HcI:0.019195,Ciona_intestinalis_HcH:0.022966):0.031537):0.069215,(Ciona_intestinalis_HcF:0.072348,Ciona_intestinalis_HcE:0.012567):0.073861):0.042874,Ciona_intestinalis_HcG:0.139841):0.19143,Ciona_intestinalis_HcA:3.0E-6):0.173095,Ciona_intestinalis_HcD:0.044654):0.081971,Ciona_intestinalis_HcB:0.043112,Ciona_intestinalis_HcC:6.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61724] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_24 = [&R] (((((((((((((((((((((Streptomyces_tsukubaensis_tyr:0.207716,Streptomyces_venezuelae_tyr:0.188261):0.203402,(Candidatus_nitrosopumilus_tyr:0.425272,(Bacillus_megaterium_tyr1:2.0E-6,Bacillus_megaterium_tyr2:0.01881):0.192134):0.122738):0.155251,(Polysphondylium_pallidum_tyr1:0.925257,Nitrosomonas_europeae_tyr:0.280817):0.395096):0.141467,Caenorhabditis_remanei_TYR5:0.437017):0.207195,(((((Pinctada_fucata_tyr3:0.024313,Pinctada_fucata_tyr2:1.0E-6):0.139827,Pinctada_fucata_tyr4:0.114919):0.181427,Pinctada_fucata_tyr1:0.349469):0.238079,(Phragmatopoma_californica_tyr:0.346402,(Dictyostelium_discoideum_tyr1:0.00944,Dictyostelium_discoideum_tyr2:0.00635):0.704224):0.196886):0.305133,Lottia_gigantea_tyr2:0.397731):0.094753):0.333252,Lottia_gigantea_tyr1:0.16869):0.022513,((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):5.0E-6,Sepia_officinalis_tyr:0.042114):0.479949):0.147619,(((Nematostella_vectensis_tyr4:0.1598,Nematostella_vectensis_tyr3:0.445716):0.284273,Nematostella_vectensis_tyr1:0.659952):0.128073,(Nematostella_vectensis_tyr2:0.532788,Hydra_magnipapillata_tyr:0.737179):0.067724):0.745602):0.222431,Brugia_malayi_TYR4:0.078892):0.08486,((Caenorhabditis_elegans_TYR2:0.0,(Caenorhabditis_remanei_TYR2:0.008374,Caenorhabditis_briggsae_TYR2:0.008832):0.008941):0.107376,(Brugia_malayi_TYR3:0.363219,((Caenorhabditis_remanei_TYR1:0.0,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.023795):0.023816,Caenorhabditis_elegans_TYR1:0.0):0.194994):0.163235):0.052507):0.09532,((((Caenorhabditis_elgans_TYR4:0.016722,Caenorhabditis_remanei_TYR4:0.0):0.047022,(Caenorhabditis_remanei_TYR3:0.025457,(Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_elegans_TYR3:0.016872):0.0):0.137255):0.011543,Caenorhabditis_briggsae_TYR4:1.0E-6):0.130266,Brugia_malayi_TYR1:0.120295):0.112186):0.032909,Brugia_malayi_TYR2:0.150682):0.193855,(Caenorhabditis_elegans_TYR5:0.008554,Caenorhabditis_briggsae_TYR6:0.0):0.720858):0.346631,((((Ectocarpus_siliculosus_tyr12:0.062926,Ectocarpus_siliculosus_tyr13:1.0E-6):0.235711,(((Ectocarpus_siliculosus_tyr18:0.128825,Ectocarpus_siliculosus_tyr16:2.0E-6):0.036267,(Ectocarpus_siliculosus_tyr17:0.070903,Ectocarpus_siliculosus_tyr15:0.257284):0.039257):0.117325,Ectocarpus_siliculosus_tyr14:0.080367):0.360232):0.108592,(((Ectocarpus_siliculosus_tyr2:0.055571,Ectocarpus_siliculosus_tyr3:0.031554):0.100945,Ectocarpus_siliculosus_tyr1:0.116692):0.032018,((Ectocarpus_siliculosus_tyr6:0.186826,Ectocarpus_siliculosus_tyr5:0.171159):0.234816,Ectocarpus_siliculosus_tyr4:0.133291):0.027669):0.597745):0.180935,((Ectocarpus_siliculosus_tyr8:0.124943,((Ectocarpus_siliculosus_tyr10:0.079051,Ectocarpus_siliculosus_tyr11:0.030533):0.032459,Ectocarpus_siliculosus_tyr9:0.052422):0.082261):0.188487,Ectocarpus_siliculosus_tyr7:0.226534):0.321947):0.979041):0.340193,Lottia_gigantea_Hc:0.596315):0.17673,((((Ciona_intestinalis_HcF:0.043928,Ciona_intestinalis_HcE:0.021793):0.042109,((Ciona_intestinalis_HcI:0.071436,Ciona_intestinalis_HcH:0.039484):0.03752,Ciona_intestinalis_HcG:0.150595):0.023422):0.266965,(Ciona_intestinalis_HcA:0.023313,((Ciona_intestinalis_HcC:0.057197,Ciona_intestinalis_HcD:0.0):0.11597,Ciona_intestinalis_HcB:0.047128):0.082012):0.101929):0.387833,(Sepia_officinalis_Hc:0.067094,(Aplysia_californica_Hc:0.164718,(Megathura_crenulata_Hc:0.201859,Nucula_nucleus_Hc:0.212083):0.041459):0.165636):0.452317):0.478091):0.365085,(((Neurospora_tetrasperma_tyr2:0.01693,Neurospora_crassa_tyr2:0.0):0.266756,((Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.018059):0.437078,(Aspergillus_aculeatus_tyr:0.406293,Agaricus_bisporus_tyr:0.5818):0.184851):0.089562):0.205562,(Neurospora_crassa_tyr1:0.026176,Neurospora_tetrasperma_tyr1:1.0E-6):0.464882):0.344778):0.930229,(((Glycine_max_CO8:0.08699,((Glycine_max_CO9:0.055035,(Glycine_max_CO12:0.056322,Glycine_max_CO11:0.0):0.011452):0.045438,Glycine_max_CO10:0.082095):0.060951):0.081711,(Glycine_max_CO1:0.0,Glycine_max_CO2:0.0):0.184283):0.015463,(Vitis_vinifera_CO:0.115853,Oryza_sativa_CO:0.149454):0.071265):2.0E-6):0.043066,(Glycine_max_CO3:0.052932,Glycine_max_CO4:0.046724):0.246609):0.108807,Glycine_max_CO5:0.204419):0.171087,Glycine_max_CO6:0.02837,Glycine_max_CO7:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61720] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_18 = [&R] (((((((((((((((((Caenorhabditis_remanei_TYR1:0.009775,Caenorhabditis_elegans_TYR1:0.01997):0.020032,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):1.0E-6):0.130464,Brugia_malayi_TYR3:0.295558):0.187571,((Brugia_malayi_TYR1:0.174649,(((Caenorhabditis_briggsae_TYR4:0.010191,(Caenorhabditis_elgans_TYR4:0.004815,(Caenorhabditis_elegans_TYR5:1.0E-6,Caenorhabditis_briggsae_TYR6:0.021214):1.169465):0.015875):0.010187,Caenorhabditis_remanei_TYR4:0.0):0.111727,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_elegans_TYR3:0.0):0.0,Caenorhabditis_remanei_TYR3:0.073572):0.194317):0.115233):0.16234,Brugia_malayi_TYR2:0.218438):0.081652):0.047591,Brugia_malayi_TYR4:0.103086):0.080467,(Caenorhabditis_briggsae_TYR2:0.024248,(Caenorhabditis_elegans_TYR2:0.011582,Caenorhabditis_remanei_TYR2:0.009173):0.034206):0.027231):0.293966,((((Lottia_gigantea_tyr2:0.888072,Pinctada_fucata_tyr1:0.619331):0.195685,(Pinctada_fucata_tyr4:0.141675,(Pinctada_fucata_tyr2:0.0,Pinctada_fucata_tyr3:0.01019):0.22326):0.369896):0.396917,(Lottia_gigantea_tyr1:0.318275,((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.044254,Sepia_officinalis_tyr:0.033014):0.646702):0.148151):0.230022,Phragmatopoma_californica_tyr:0.635113):0.229222):0.383328,Caenorhabditis_remanei_TYR5:0.683798):0.301432,(((Ectocarpus_siliculosus_tyr12:0.235877,Ectocarpus_siliculosus_tyr13:1.0E-6):0.558329,((Ectocarpus_siliculosus_tyr2:2.0E-6,((Ectocarpus_siliculosus_tyr3:2.0E-6,((Ectocarpus_siliculosus_tyr6:0.138555,Ectocarpus_siliculosus_tyr5:0.291473):0.414373,Ectocarpus_siliculosus_tyr4:0.250184):0.197427):0.174782,Ectocarpus_siliculosus_tyr1:0.248071):0.042462):0.744237,(Ectocarpus_siliculosus_tyr14:0.111466,((Ectocarpus_siliculosus_tyr18:0.132889,(Ectocarpus_siliculosus_tyr16:0.083952,Ectocarpus_siliculosus_tyr17:0.195557):0.035408):0.226919,Ectocarpus_siliculosus_tyr15:0.256311):0.083542):0.254873):0.145945):0.262041,((((Ectocarpus_siliculosus_tyr9:0.079961,Ectocarpus_siliculosus_tyr11:5.0E-6):0.01945,Ectocarpus_siliculosus_tyr10:0.193705):0.071336,Ectocarpus_siliculosus_tyr8:0.20545):0.230921,Ectocarpus_siliculosus_tyr7:0.148286):0.359873):0.95606):0.208134,(((((Streptomyces_tsukubaensis_tyr:0.11765,Streptomyces_venezuelae_tyr:0.224734):0.200341,Nitrosomonas_europeae_tyr:0.715219):0.107392,(Candidatus_nitrosopumilus_tyr:0.672472,(Dictyostelium_discoideum_tyr2:0.0,Dictyostelium_discoideum_tyr1:0.0):0.848983):0.291314):0.138522,(Bacillus_megaterium_tyr2:0.010425,Bacillus_megaterium_tyr1:1.0E-6):0.39318):0.029821,Polysphondylium_pallidum_tyr1:0.732403):0.380841):0.144036,((Nematostella_vectensis_tyr1:0.736479,(Hydra_magnipapillata_tyr:0.488636,Nematostella_vectensis_tyr2:1.524417):0.459872):0.13879,(Nematostella_vectensis_tyr3:0.317495,Nematostella_vectensis_tyr4:0.351914):0.261904):0.973467):0.249533,((((Glycine_max_CO5:0.423974,(((((((Glycine_max_CO12:0.05621,Glycine_max_CO11:0.0):0.009563,Glycine_max_CO9:0.124862):0.070448,Glycine_max_CO10:0.143691):0.005157,(Glycine_max_CO7:0.026261,Glycine_max_CO6:0.008207):0.29313):0.182755,Glycine_max_CO8:0.174762):0.045265,Oryza_sativa_CO:0.173595):0.096023,(Vitis_vinifera_CO:0.187837,(Glycine_max_CO4:0.024047,Glycine_max_CO3:0.116902):0.216281):0.046994):0.099837):0.18415,(Glycine_max_CO1:0.0,Glycine_max_CO2:0.0):4.0E-6):2.042701,((Nucula_nucleus_Hc:0.358863,(Megathura_crenulata_Hc:0.410498,Aplysia_californica_Hc:0.106987):0.120632):0.215311,Sepia_officinalis_Hc:0.074004):0.739403):0.078451,(((Ciona_intestinalis_HcG:0.098515,(Ciona_intestinalis_HcH:0.029994,Ciona_intestinalis_HcI:0.1345):0.095171):1.4E-5,(Ciona_intestinalis_HcE:1.0E-6,Ciona_intestinalis_HcF:0.17622):0.102133):0.113461,(Ciona_intestinalis_HcA:0.009069,((Ciona_intestinalis_HcC:0.0,Ciona_intestinalis_HcB:0.048068):0.108518,Ciona_intestinalis_HcD:0.080924):0.112773):0.290137):0.729452):0.354647):0.536099,Lottia_gigantea_Hc:1.395076):0.220414,Aspergillus_aculeatus_tyr:0.422259):0.476514,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.020328):0.411655):0.214994,((Neurospora_tetrasperma_tyr1:0.009906,Neurospora_crassa_tyr1:0.0):0.600345,Agaricus_bisporus_tyr:0.768064):0.207082):0.509058,Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.009802); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61714] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_15 = [&R] (((((((((((((((Caenorhabditis_elegans_TYR5:0.009395,Caenorhabditis_briggsae_TYR6:0.0):1.097721,((Caenorhabditis_remanei_TYR3:0.043576,(Caenorhabditis_elegans_TYR3:0.008505,Caenorhabditis_briggsae_TYR3:1.0E-6):1.0E-6):0.221709,((Caenorhabditis_elgans_TYR4:0.035152,Caenorhabditis_remanei_TYR4:0.0):0.043373,Caenorhabditis_briggsae_TYR4:1.0E-6):0.024959):0.134715):0.015567,(Brugia_malayi_TYR2:0.615238,(Brugia_malayi_TYR3:0.170588,(((Caenorhabditis_remanei_TYR1:0.009559,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.026585):0.02702,Caenorhabditis_elegans_TYR1:1.0E-6):0.186814,(((Caenorhabditis_briggsae_TYR2:0.01887,Caenorhabditis_remanei_TYR2:1.0E-6):0.02836,Caenorhabditis_elegans_TYR2:1.0E-6):0.054941,Brugia_malayi_TYR4:0.287493):0.193662):0.073723):0.093416):0.039825):0.011778,Brugia_malayi_TYR1:0.16514):0.291341,Caenorhabditis_remanei_TYR5:0.625012):0.308821,(((Lottia_gigantea_tyr2:1.071281,(Pinctada_fucata_tyr1:0.361188,((Pinctada_fucata_tyr2:2.0E-6,Pinctada_fucata_tyr3:0.035762):0.225317,Pinctada_fucata_tyr4:0.158488):0.462801):0.30053):0.211783,Lottia_gigantea_tyr1:0.392425):0.129777,((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:1.0E-6):0.062253,Sepia_officinalis_tyr:0.037585):0.470567):0.201445):0.10122,((Nematostella_vectensis_tyr2:1.124449,((Hydra_magnipapillata_tyr:1.248612,Nematostella_vectensis_tyr3:0.252394):0.232851,Nematostella_vectensis_tyr4:0.317406):0.457747):0.207766,Nematostella_vectensis_tyr1:0.73444):1.064094):0.151478,((((Nitrosomonas_europeae_tyr:0.741638,Polysphondylium_pallidum_tyr1:0.633175):0.462637,((Bacillus_megaterium_tyr1:0.0,Bacillus_megaterium_tyr2:0.0292):0.391088,(Streptomyces_tsukubaensis_tyr:0.355669,Streptomyces_venezuelae_tyr:0.428124):0.337956):0.161525):0.19221,(Dictyostelium_discoideum_tyr1:0.0,Dictyostelium_discoideum_tyr2:0.017796):0.739819):0.100149,(Candidatus_nitrosopumilus_tyr:0.67523,Phragmatopoma_californica_tyr:0.829172):0.139609):0.197854):0.358423,(((((Glycine_max_CO6:0.0,Glycine_max_CO7:0.0):0.307086,Glycine_max_CO5:0.342321):0.192987,(Glycine_max_CO3:0.073208,Glycine_max_CO4:0.080071):0.212283):0.062843,(((Glycine_max_CO1:1.0E-6,Glycine_max_CO2:0.009653):0.211104,((Glycine_max_CO8:0.125592,(Glycine_max_CO9:0.09384,((Glycine_max_CO12:0.067,Glycine_max_CO11:0.0):0.009899,Glycine_max_CO10:0.128881):0.046298):0.136673):0.130471,Oryza_sativa_CO:0.149043):0.035014):0.092329,Vitis_vinifera_CO:0.284672):2.0E-6):1.312126,Lottia_gigantea_Hc:0.88462):0.855565):0.40102,(((Ciona_intestinalis_HcI:0.094592,(Ciona_intestinalis_HcF:0.11438,Ciona_intestinalis_HcE:0.017541):0.094467):0.038553,(Ciona_intestinalis_HcG:0.063091,Ciona_intestinalis_HcH:0.061959):0.026648):0.1874,(((Ciona_intestinalis_HcC:0.185338,Ciona_intestinalis_HcD:0.007425):0.152281,Ciona_intestinalis_HcB:0.112133):0.030278,Ciona_intestinalis_HcA:6.0E-6):0.127736):0.511027):0.264665,(Sepia_officinalis_Hc:0.159623,(Nucula_nucleus_Hc:0.336331,(Megathura_crenulata_Hc:0.232934,Aplysia_californica_Hc:0.189572):0.142923):0.077384):0.326833):0.57897,(((Ectocarpus_siliculosus_tyr12:0.162559,Ectocarpus_siliculosus_tyr13:1.2E-5):0.359722,((((Ectocarpus_siliculosus_tyr8:0.227002,Ectocarpus_siliculosus_tyr9:0.036029):0.066246,(Ectocarpus_siliculosus_tyr11:1.0E-6,Ectocarpus_siliculosus_tyr10:0.106449):0.011039):0.22838,Ectocarpus_siliculosus_tyr7:0.217064):0.463812,((((Ectocarpus_siliculosus_tyr2:0.071615,Ectocarpus_siliculosus_tyr3:0.100947):0.153085,Ectocarpus_siliculosus_tyr1:0.272292):0.082172,Ectocarpus_siliculosus_tyr4:0.248998):0.070449,(Ectocarpus_siliculosus_tyr6:0.338784,Ectocarpus_siliculosus_tyr5:0.215216):0.309528):0.431413):0.384196):0.333232,(Ectocarpus_siliculosus_tyr15:0.120132,(Ectocarpus_siliculosus_tyr18:0.174335,(Ectocarpus_siliculosus_tyr17:0.159645,(Ectocarpus_siliculosus_tyr16:0.051301,Ectocarpus_siliculosus_tyr14:0.272869):0.055596):0.037923):0.203762):0.182381):0.940659):0.728465,Aspergillus_aculeatus_tyr:0.330943):0.218015,((Agaricus_bisporus_tyr:0.409358,(Neurospora_tetrasperma_tyr3:0.017042,Neurospora_crassa_tyr3:0.0):0.517783):0.304679,(Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.009199):0.446622):0.087134):0.704855,Neurospora_tetrasperma_tyr2:0.01807,Neurospora_crassa_tyr2:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61711] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_11 = [&R] (((((((((((((((((((Caenorhabditis_elegans_TYR3:0.017399,Caenorhabditis_briggsae_TYR3:0.0):2.0E-6,Caenorhabditis_remanei_TYR3:0.035601):0.205086,((Caenorhabditis_elgans_TYR4:0.01719,Caenorhabditis_remanei_TYR4:0.008178):0.034109,Caenorhabditis_briggsae_TYR4:0.0):0.121489):0.13011,((((((Caenorhabditis_briggsae_TYR2:0.02691,Caenorhabditis_remanei_TYR2:1.0E-6):0.017589,Caenorhabditis_elegans_TYR2:1.0E-6):0.109586,Brugia_malayi_TYR4:0.280764):0.113681,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.024696,Caenorhabditis_remanei_TYR1:0.0):0.016677,Caenorhabditis_elegans_TYR1:0.0):0.09576):0.058495,Brugia_malayi_TYR3:0.224125):0.02672,Brugia_malayi_TYR2:0.24247):0.045626):0.01154,(Brugia_malayi_TYR1:0.097861,(Caenorhabditis_elegans_TYR5:0.028598,Caenorhabditis_briggsae_TYR6:0.00679):0.698404):0.011914):0.136776,((((Sepia_officinalis_tyr:0.155175,(Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:1.0E-6):0.023586):0.805862,((Lottia_gigantea_tyr2:0.597704,(((Phragmatopoma_californica_tyr:1.085805,Pinctada_fucata_tyr3:2.0E-6):0.017832,Pinctada_fucata_tyr2:1.0E-6):0.202628,Pinctada_fucata_tyr4:0.133676):0.434167):0.103041,Pinctada_fucata_tyr1:0.483746):0.162076):0.09405,Lottia_gigantea_tyr1:0.301042):0.337646,Caenorhabditis_remanei_TYR5:0.636014):0.229926):0.061065,((((Ectocarpus_siliculosus_tyr16:0.039366,Ectocarpus_siliculosus_tyr17:0.068605):1.0E-6,Ectocarpus_siliculosus_tyr15:0.291129):0.038686,Ectocarpus_siliculosus_tyr18:0.093499):0.08752,(Ectocarpus_siliculosus_tyr14:0.078821,(((((Ectocarpus_siliculosus_tyr6:0.221282,Ectocarpus_siliculosus_tyr5:0.327476):0.229881,Ectocarpus_siliculosus_tyr4:0.203642):0.048181,((Ectocarpus_siliculosus_tyr2:0.074848,Ectocarpus_siliculosus_tyr3:0.066454):0.15875,Ectocarpus_siliculosus_tyr1:0.151596):0.070359):0.472921,((((Ectocarpus_siliculosus_tyr10:0.142578,Ectocarpus_siliculosus_tyr11:0.001777):0.061838,Ectocarpus_siliculosus_tyr7:0.3015):0.032988,Ectocarpus_siliculosus_tyr9:0.034009):0.079877,Ectocarpus_siliculosus_tyr8:0.105348):0.435918):0.317618,(Ectocarpus_siliculosus_tyr13:0.033265,Ectocarpus_siliculosus_tyr12:0.070398):0.310831):0.298986):0.040196):0.888065):0.106871,((Nematostella_vectensis_tyr1:0.683573,(Nematostella_vectensis_tyr4:0.244055,Nematostella_vectensis_tyr3:0.397095):0.208247):4.0E-6,(Hydra_magnipapillata_tyr:0.720944,Nematostella_vectensis_tyr2:0.630007):0.295285):0.890619):0.10698,(Streptomyces_tsukubaensis_tyr:0.35973,Streptomyces_venezuelae_tyr:0.074503):0.109145):0.121354,(((Polysphondylium_pallidum_tyr1:0.453072,Nitrosomonas_europeae_tyr:0.531868):0.01153,(Bacillus_megaterium_tyr1:0.0,Bacillus_megaterium_tyr2:0.0):0.263999):0.161471,(Dictyostelium_discoideum_tyr2:1.0E-6,Dictyostelium_discoideum_tyr1:0.007782):0.547107):0.039578):0.070418,Candidatus_nitrosopumilus_tyr:0.391549):0.617354,((Megathura_crenulata_Hc:0.116832,(Aplysia_californica_Hc:0.130261,(Sepia_officinalis_Hc:0.186213,Nucula_nucleus_Hc:0.164421):0.175937):0.068704):0.32496,(((Ciona_intestinalis_HcF:0.107637,Ciona_intestinalis_HcE:0.034764):0.121781,(Ciona_intestinalis_HcG:0.242401,(Ciona_intestinalis_HcI:0.138752,Ciona_intestinalis_HcH:0.082358):0.088807):0.080827):0.117852,((Ciona_intestinalis_HcD:0.042314,(Ciona_intestinalis_HcB:0.069714,Ciona_intestinalis_HcC:0.027219):0.0372):5.0E-6,Ciona_intestinalis_HcA:0.167107):0.196631):0.459863):0.524969):0.154917,((Aspergillus_aculeatus_tyr:0.30772,Agaricus_bisporus_tyr:0.383623):0.07897,(((Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.0):0.561963,(Neurospora_crassa_tyr2:1.0E-6,Neurospora_tetrasperma_tyr2:0.028161):0.447289):0.162227,(Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0):0.521097):0.115171):0.309098):0.375942,Lottia_gigantea_Hc:0.394826):1.035479,((Glycine_max_CO3:0.046749,Glycine_max_CO4:0.026987):0.136171,Vitis_vinifera_CO:0.150158):1.0E-6):0.027109,((Glycine_max_CO2:0.00848,Glycine_max_CO1:0.0):0.052038,Glycine_max_CO5:0.315242):0.090151):0.053956,Oryza_sativa_CO:0.145398):0.029654,((((Glycine_max_CO10:0.056313,Glycine_max_CO9:0.047236):0.016997,Glycine_max_CO11:1.0E-6):0.017819,Glycine_max_CO12:0.01753):0.037749,Glycine_max_CO8:0.17688):0.040775):0.216477,Glycine_max_CO6:0.010647,Glycine_max_CO7:0.009779); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61707] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_6 = [&R] (((((((((((((((((Caenorhabditis_elgans_TYR4:0.019829,Caenorhabditis_remanei_TYR4:0.029102):0.039136,Caenorhabditis_briggsae_TYR4:2.0E-6):0.10499,(Caenorhabditis_elegans_TYR3:0.028108,(Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.061598):0.02307):0.218997):0.062855,Brugia_malayi_TYR1:0.208107):3.0E-6,((Brugia_malayi_TYR3:0.331788,((((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.028866,Caenorhabditis_remanei_TYR1:0.011634):0.040908,Caenorhabditis_elegans_TYR1:1.0E-6):0.14899,((Caenorhabditis_elegans_TYR2:1.0E-6,(Caenorhabditis_remanei_TYR2:0.008598,Caenorhabditis_briggsae_TYR2:0.047208):0.022577):0.052832,Brugia_malayi_TYR4:0.178604):0.121965):0.119173):0.083861,Brugia_malayi_TYR2:0.301177):0.123489):3.0E-6,(Caenorhabditis_briggsae_TYR6:3.0E-6,Caenorhabditis_elegans_TYR5:0.063833):1.105739):0.169864,Caenorhabditis_remanei_TYR5:1.077797):0.344707,((Lottia_gigantea_tyr2:0.843813,((Pinctada_fucata_tyr4:0.141617,(Pinctada_fucata_tyr3:0.039546,Pinctada_fucata_tyr2:1.0E-6):0.246983):0.41081,Pinctada_fucata_tyr1:0.344223):0.115435):0.125661,(((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.067515,Sepia_officinalis_tyr:0.05213):0.477336,Lottia_gigantea_tyr1:0.273672):0.262451):0.254461):0.098419,Phragmatopoma_californica_tyr:0.338178):0.139965,((((Polysphondylium_pallidum_tyr1:0.958171,(Bacillus_megaterium_tyr2:0.010162,Bacillus_megaterium_tyr1:1.0E-6):0.472191):0.047391,(Nitrosomonas_europeae_tyr:0.443736,(Streptomyces_venezuelae_tyr:0.317949,Streptomyces_tsukubaensis_tyr:0.306867):0.304566):0.150519):0.482162,((((((Ectocarpus_siliculosus_tyr1:0.144052,(Ectocarpus_siliculosus_tyr2:0.022264,Ectocarpus_siliculosus_tyr3:0.125877):0.189587):0.183226,(Ectocarpus_siliculosus_tyr4:0.377185,(Ectocarpus_siliculosus_tyr6:0.233171,Ectocarpus_siliculosus_tyr5:0.220945):0.262339):0.078966):0.479743,((((Ectocarpus_siliculosus_tyr10:0.175786,Ectocarpus_siliculosus_tyr9:0.028108):0.061118,Ectocarpus_siliculosus_tyr11:0.017554):0.030274,Ectocarpus_siliculosus_tyr8:0.159726):0.202463,Ectocarpus_siliculosus_tyr7:0.171253):0.494405):0.37856,(Ectocarpus_siliculosus_tyr13:2.0E-6,Ectocarpus_siliculosus_tyr12:0.220383):0.458432):0.083009,(((Ectocarpus_siliculosus_tyr18:0.172945,(Ectocarpus_siliculosus_tyr17:0.080779,Ectocarpus_siliculosus_tyr16:0.097093):0.032142):0.095903,Ectocarpus_siliculosus_tyr14:0.120906):0.111619,Ectocarpus_siliculosus_tyr15:0.253305):0.187158):0.965497,Candidatus_nitrosopumilus_tyr:0.710125):0.101098):0.115626,(Dictyostelium_discoideum_tyr1:0.0,Dictyostelium_discoideum_tyr2:0.008985):0.638504):0.082569):0.325108,((Nematostella_vectensis_tyr1:1.169028,(Hydra_magnipapillata_tyr:0.962951,Nematostella_vectensis_tyr2:1.1637):0.251165):0.040211,(Nematostella_vectensis_tyr4:0.479218,Nematostella_vectensis_tyr3:0.573303):0.297188):1.101634):0.256269,(((((Aplysia_californica_Hc:0.196626,Megathura_crenulata_Hc:0.274842):0.06181,Nucula_nucleus_Hc:0.193979):0.076291,Sepia_officinalis_Hc:0.151579):0.729393,(((Ciona_intestinalis_HcG:0.145558,(Ciona_intestinalis_HcI:0.097036,Ciona_intestinalis_HcH:0.091239):0.171435):0.063647,(Ciona_intestinalis_HcE:0.014926,Ciona_intestinalis_HcF:0.141504):0.181152):0.255806,(Ciona_intestinalis_HcA:0.0,((Ciona_intestinalis_HcD:4.0E-6,Ciona_intestinalis_HcC:0.205584):0.215324,Ciona_intestinalis_HcB:0.242873):0.039452):0.102849):0.444744):0.461609,Lottia_gigantea_Hc:0.528098):0.274557):0.322332,(((Vitis_vinifera_CO:0.177245,Oryza_sativa_CO:0.267546):0.058103,(((((Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.04903):0.035168,Glycine_max_CO10:0.169059):0.07406,(Glycine_max_CO9:0.045178,Glycine_max_CO8:0.173269):0.065914):0.092156,(Glycine_max_CO5:0.197007,(Glycine_max_CO6:0.020174,Glycine_max_CO7:1.0E-6):0.315011):0.087636):0.042564,(Glycine_max_CO4:0.067297,Glycine_max_CO3:0.005303):0.29058):0.057895):0.021982,(Glycine_max_CO1:0.0,Glycine_max_CO2:0.0):0.186475):1.136698):0.362355,(Neurospora_crassa_tyr3:1.0E-6,Neurospora_tetrasperma_tyr3:0.019016):0.303065):0.165373,(Aspergillus_aculeatus_tyr:0.767028,(Neurospora_tetrasperma_tyr2:0.028668,Neurospora_crassa_tyr2:0.0):0.539715):0.17419):0.219625,Agaricus_bisporus_tyr:0.526375):0.685328,Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61702] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_16 = [&R] ((((((((((((((((Brugia_malayi_TYR3:0.216917,(Caenorhabditis_elegans_TYR5:0.030106,Caenorhabditis_briggsae_TYR6:1.9E-5):1.215689):0.081781,((((Caenorhabditis_remanei_TYR4:1.0E-6,(Caenorhabditis_elgans_TYR4:0.009702,Caenorhabditis_briggsae_TYR4:0.028915):0.028817):0.118511,((Caenorhabditis_elegans_TYR3:0.020526,Caenorhabditis_briggsae_TYR3:1.0E-6):1.0E-6,Caenorhabditis_remanei_TYR3:0.062386):0.216977):0.267491,Brugia_malayi_TYR1:0.280531):0.012981,((Brugia_malayi_TYR4:0.138585,(((Caenorhabditis_elegans_TYR2:0.0,Caenorhabditis_remanei_TYR2:0.0):0.025617,Caenorhabditis_briggsae_TYR2:0.019459):0.102091,((Caenorhabditis_remanei_TYR1:0.0,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.038403):0.047994,Caenorhabditis_elegans_TYR1:0.0):0.155804):0.04129):0.13568,Brugia_malayi_TYR2:0.249243):0.063291):0.191169):0.234028,Caenorhabditis_remanei_TYR5:0.688469):0.280072,((((Nematostella_vectensis_tyr1:0.832459,(Nematostella_vectensis_tyr2:1.219412,Hydra_magnipapillata_tyr:0.487625):0.270304):0.091772,(Nematostella_vectensis_tyr3:0.313493,Nematostella_vectensis_tyr4:0.387678):0.187715):0.772292,(((Ectocarpus_siliculosus_tyr12:0.155858,Ectocarpus_siliculosus_tyr13:1.0E-6):0.269816,((((Ectocarpus_siliculosus_tyr3:0.135203,Ectocarpus_siliculosus_tyr2:0.068816):0.102493,Ectocarpus_siliculosus_tyr1:0.243536):0.08818,((Ectocarpus_siliculosus_tyr5:0.270874,Ectocarpus_siliculosus_tyr6:0.158779):0.431771,Ectocarpus_siliculosus_tyr4:0.251065):0.192682):0.62156,((((Ectocarpus_siliculosus_tyr9:0.023328,Ectocarpus_siliculosus_tyr11:0.039711):0.022476,Ectocarpus_siliculosus_tyr8:0.217812):0.083447,Ectocarpus_siliculosus_tyr10:0.048232):0.335275,Ectocarpus_siliculosus_tyr7:0.163745):0.307256):0.203949):0.317202,((((Ectocarpus_siliculosus_tyr16:0.142504,Ectocarpus_siliculosus_tyr17:0.069415):0.043288,Ectocarpus_siliculosus_tyr18:0.042202):0.169221,Ectocarpus_siliculosus_tyr14:0.188111):0.142299,Ectocarpus_siliculosus_tyr15:0.168589):0.111157):0.740409):5.0E-6,((((Ciona_intestinalis_HcG:0.382224,(((Ciona_intestinalis_HcC:0.136726,Ciona_intestinalis_HcD:2.0E-6):0.241503,Ciona_intestinalis_HcB:0.219652):0.06665,Ciona_intestinalis_HcA:0.092736):0.217195):0.121893,(((Ciona_intestinalis_HcF:0.112823,Ciona_intestinalis_HcE:0.055966):0.150881,Lottia_gigantea_Hc:1.148087):4.1E-5,(Ciona_intestinalis_HcI:0.021796,Ciona_intestinalis_HcH:0.031131):0.196796):0.147703):0.562082,(((Nucula_nucleus_Hc:0.193419,Megathura_crenulata_Hc:0.285992):0.019814,Aplysia_californica_Hc:0.113198):0.100596,Sepia_officinalis_Hc:0.058387):0.410091):0.280208,((((Neurospora_tetrasperma_tyr2:0.01015,Neurospora_crassa_tyr2:0.0):0.429858,(Aspergillus_aculeatus_tyr:0.537639,(Neurospora_tetrasperma_tyr3:0.043963,Neurospora_crassa_tyr3:1.0E-6):0.393905):0.195211):0.160328,(Neurospora_tetrasperma_tyr1:0.009931,Neurospora_crassa_tyr1:0.0):0.458777):0.075601,Agaricus_bisporus_tyr:0.431943):0.524318):0.62159):0.192596):0.047969,Polysphondylium_pallidum_tyr1:0.468816):0.388427,(Phragmatopoma_californica_tyr:0.693964,(((Streptomyces_tsukubaensis_tyr:0.31509,Streptomyces_venezuelae_tyr:0.222182):0.477562,((Candidatus_nitrosopumilus_tyr:0.445436,(Bacillus_megaterium_tyr1:1.0E-6,Bacillus_megaterium_tyr2:0.010886):0.577167):6.0E-6,Nitrosomonas_europeae_tyr:0.650818):0.205892):0.088164,(Dictyostelium_discoideum_tyr2:1.0E-6,Dictyostelium_discoideum_tyr1:0.009878):0.521879):0.135115):2.4E-5):0.293865,(((((Pinctada_fucata_tyr2:0.0,Pinctada_fucata_tyr3:0.0):0.37474,Pinctada_fucata_tyr4:0.124316):0.636086,Pinctada_fucata_tyr1:0.574539):0.199123,Lottia_gigantea_tyr2:0.562235):0.055853,((Sepia_officinalis_tyr:0.112055,(Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):1.0E-6):0.554217,Lottia_gigantea_tyr1:0.396947):0.782337):0.319254):1.173171,Glycine_max_CO2:4.0E-6):0.031568,Glycine_max_CO1:0.0):0.068805,Glycine_max_CO5:0.118066):0.079044,((Glycine_max_CO11:0.05777,Glycine_max_CO12:0.008686):0.13459,Glycine_max_CO10:0.018033):0.156429):0.053072,Oryza_sativa_CO:0.05925):0.061796,(Glycine_max_CO9:0.146001,Glycine_max_CO8:0.055795):0.067721):0.058822,Vitis_vinifera_CO:0.129653):0.085841,(Glycine_max_CO6:0.019461,Glycine_max_CO7:0.027665):0.326515):0.259896,Glycine_max_CO3:0.032188,Glycine_max_CO4:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61712] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_12 = [&R] (((((((((((((((((((Ectocarpus_siliculosus_tyr10:0.149248,Ectocarpus_siliculosus_tyr11:0.044085):0.068414,(Ectocarpus_siliculosus_tyr9:0.017227,Ectocarpus_siliculosus_tyr8:0.269852):3.0E-6):0.298396,(((((Ectocarpus_siliculosus_tyr3:0.062217,Ectocarpus_siliculosus_tyr2:0.084182):0.152044,Ectocarpus_siliculosus_tyr1:0.165906):0.21642,Ectocarpus_siliculosus_tyr4:0.101044):0.246308,(Ectocarpus_siliculosus_tyr6:0.113229,Ectocarpus_siliculosus_tyr5:0.441585):0.292524):0.82956,Ectocarpus_siliculosus_tyr7:0.250139):0.154948):0.290403,((Ectocarpus_siliculosus_tyr12:0.149683,Ectocarpus_siliculosus_tyr13:0.022371):0.236146,((((Ectocarpus_siliculosus_tyr18:0.219727,Ectocarpus_siliculosus_tyr17:0.111389):0.008124,Ectocarpus_siliculosus_tyr16:0.105693):0.097273,Ectocarpus_siliculosus_tyr15:0.337255):0.144206,Ectocarpus_siliculosus_tyr14:0.104998):0.400369):0.353116):0.660546,((Dictyostelium_discoideum_tyr1:0.020109,Dictyostelium_discoideum_tyr2:1.0E-6):0.666912,Phragmatopoma_californica_tyr:0.609679):0.24139):0.23706,(Lottia_gigantea_tyr2:1.036239,((Pinctada_fucata_tyr4:0.019912,(Pinctada_fucata_tyr3:0.0,Pinctada_fucata_tyr2:0.0):0.317731):0.572534,Pinctada_fucata_tyr1:0.708132):0.169266):0.254285):1.0E-6,((((((Caenorhabditis_remanei_TYR4:0.009321,Caenorhabditis_elgans_TYR4:0.020503):0.081453,Caenorhabditis_briggsae_TYR4:1.0E-6):0.095707,((Caenorhabditis_elegans_TYR3:0.042101,Caenorhabditis_briggsae_TYR3:0.0):0.004357,Caenorhabditis_remanei_TYR3:0.038619):0.284272):0.160193,(((((((Caenorhabditis_briggsae_TYR2:0.022502,Caenorhabditis_remanei_TYR2:0.00957):0.022461,Caenorhabditis_elegans_TYR2:0.0):0.131563,Brugia_malayi_TYR4:0.222929):0.140762,(Caenorhabditis_elegans_TYR1:0.0,(Caenorhabditis_remanei_TYR1:0.0,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.039039):0.019112):0.225374):0.120211,Brugia_malayi_TYR1:0.293968):0.094443,Brugia_malayi_TYR2:0.315474):2.0E-6,Brugia_malayi_TYR3:0.367004):0.101425):0.124946,Caenorhabditis_remanei_TYR5:0.959614):0.124339,(Lottia_gigantea_tyr1:0.325592,((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.031868,Sepia_officinalis_tyr:0.116589):0.854534):0.430366):0.311157):0.144278,((((Nematostella_vectensis_tyr3:0.494179,Nematostella_vectensis_tyr4:0.221643):0.330479,(Nematostella_vectensis_tyr2:1.156821,Hydra_magnipapillata_tyr:0.509837):0.491838):0.211151,Nematostella_vectensis_tyr1:0.685513):0.573129,(Polysphondylium_pallidum_tyr1:0.616684,((((Bacillus_megaterium_tyr1:2.0E-6,Bacillus_megaterium_tyr2:0.010714):0.533128,Candidatus_nitrosopumilus_tyr:0.817034):0.115313,(Streptomyces_tsukubaensis_tyr:0.318067,Streptomyces_venezuelae_tyr:0.274028):0.165102):0.266992,Nitrosomonas_europeae_tyr:0.903188):0.200957):0.279033):0.211632):0.293214,(Glycine_max_CO4:8.0E-6,(((Vitis_vinifera_CO:0.270502,((((Glycine_max_CO10:0.182309,(Glycine_max_CO9:0.032694,(Glycine_max_CO12:0.083206,Glycine_max_CO11:1.0E-6):0.01143):0.031754):0.071238,Glycine_max_CO8:0.073362):0.048939,Oryza_sativa_CO:0.145098):0.06321,(Glycine_max_CO2:0.009718,Glycine_max_CO1:0.0):0.204703):0.004835):0.075568,((Glycine_max_CO7:0.011833,Glycine_max_CO6:0.009564):0.208486,Glycine_max_CO5:0.241679):0.202914):0.201631,Glycine_max_CO3:0.023487):0.075224):1.995763):0.331804,((Neurospora_tetrasperma_tyr3:0.010276,Neurospora_crassa_tyr3:1.0E-6):0.601005,(((Neurospora_tetrasperma_tyr1:0.01954,Neurospora_crassa_tyr1:0.0):0.514962,Agaricus_bisporus_tyr:0.466303):0.350541,(Aspergillus_aculeatus_tyr:0.520785,(Neurospora_crassa_tyr2:1.0E-6,Neurospora_tetrasperma_tyr2:0.051225):0.668795):0.205218):1.4E-5):0.582897):0.209209,(Caenorhabditis_briggsae_TYR6:3.0E-6,Caenorhabditis_elegans_TYR5:0.020798):1.122231):0.373402,Lottia_gigantea_Hc:0.636755):0.374833,((Sepia_officinalis_Hc:0.191897,Megathura_crenulata_Hc:0.577344):0.074596,(Nucula_nucleus_Hc:0.285644,Aplysia_californica_Hc:0.191537):0.058054):0.493056):0.879062,(Ciona_intestinalis_HcI:0.04707,Ciona_intestinalis_HcH:0.094254):0.052656):0.045437,(Ciona_intestinalis_HcE:0.021394,Ciona_intestinalis_HcF:0.076442):0.128428):0.07163,Ciona_intestinalis_HcG:0.1034):0.208798,Ciona_intestinalis_HcA:0.018222):0.139655,Ciona_intestinalis_HcB:0.12951):0.19318,Ciona_intestinalis_HcC:0.015567,Ciona_intestinalis_HcD:0.017504); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61708] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_21 = [&R] ((((((((((((((((((Caenorhabditis_remanei_TYR2:0.0,Caenorhabditis_elegans_TYR2:0.028421):0.03311,Caenorhabditis_briggsae_TYR2:0.036375):0.088341,(Brugia_malayi_TYR3:0.351562,(((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.043429,Caenorhabditis_remanei_TYR1:0.021848):0.036629,Caenorhabditis_elegans_TYR1:1.0E-6):0.067244):0.165011):0.03122,Brugia_malayi_TYR4:0.286242):0.126136,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.026948):0.036659,Caenorhabditis_elegans_TYR3:0.0):0.170455):2.0E-6,((((Caenorhabditis_elegans_TYR5:0.054318,Caenorhabditis_briggsae_TYR6:1.0E-6):0.783875,(Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_remanei_TYR4:0.008838,Caenorhabditis_elgans_TYR4:1.0E-6):0.017712):0.082146):0.134496,Brugia_malayi_TYR1:0.211335):0.087898,Brugia_malayi_TYR2:0.314483):0.070018):0.139643,((((Pinctada_fucata_tyr1:0.594345,Lottia_gigantea_tyr2:0.88103):0.038205,(Pinctada_fucata_tyr4:0.164263,(Pinctada_fucata_tyr3:0.019102,Pinctada_fucata_tyr2:2.0E-6):0.272728):0.430609):0.260507,(Lottia_gigantea_tyr1:0.184462,((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.023515,Sepia_officinalis_tyr:0.055776):0.585223):0.322815):0.298305,Phragmatopoma_californica_tyr:0.275127):0.248326):0.126501,Caenorhabditis_remanei_TYR5:0.573893):0.242747,((Hydra_magnipapillata_tyr:0.832993,Nematostella_vectensis_tyr2:0.714646):0.259356,((Nematostella_vectensis_tyr3:0.188217,Nematostella_vectensis_tyr1:0.890447):0.203738,Nematostella_vectensis_tyr4:0.379647):0.146891):1.107397):0.035319,(((((Ectocarpus_siliculosus_tyr1:0.203827,(Ectocarpus_siliculosus_tyr2:0.095756,Ectocarpus_siliculosus_tyr3:0.113026):0.234672):0.202087,Ectocarpus_siliculosus_tyr4:0.228067):0.147942,(Ectocarpus_siliculosus_tyr6:0.166237,Ectocarpus_siliculosus_tyr5:0.352378):0.449818):0.449235,((Ectocarpus_siliculosus_tyr14:0.137094,((Ectocarpus_siliculosus_tyr18:0.089112,(Ectocarpus_siliculosus_tyr16:0.058666,Ectocarpus_siliculosus_tyr17:0.06184):0.041421):0.084198,Ectocarpus_siliculosus_tyr15:0.158742):0.163448):0.273528,(Ectocarpus_siliculosus_tyr12:0.162047,Ectocarpus_siliculosus_tyr13:1.0E-6):0.369046):0.203368):0.091476,(((Ectocarpus_siliculosus_tyr9:0.006531,Ectocarpus_siliculosus_tyr8:0.321354):0.070585,(Ectocarpus_siliculosus_tyr10:0.155174,Ectocarpus_siliculosus_tyr11:0.024281):0.075441):0.245734,Ectocarpus_siliculosus_tyr7:0.207085):0.319632):1.370592):0.102451,((((Streptomyces_venezuelae_tyr:0.10203,Streptomyces_tsukubaensis_tyr:0.349993):0.146073,Nitrosomonas_europeae_tyr:0.593628):0.117162,(Candidatus_nitrosopumilus_tyr:0.622874,(Dictyostelium_discoideum_tyr2:0.026478,Dictyostelium_discoideum_tyr1:1.0E-6):0.622295):0.20444):0.057222,(Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.232076):0.047435):0.230222,(Polysphondylium_pallidum_tyr1:0.390743,(((Glycine_max_CO3:0.05871,Glycine_max_CO4:0.024855):0.184173,Glycine_max_CO5:0.278818):0.020911,(((Glycine_max_CO2:0.028384,Glycine_max_CO1:0.0):0.210168,(Oryza_sativa_CO:0.144708,(Glycine_max_CO8:0.094184,(Glycine_max_CO9:0.033762,((Glycine_max_CO12:0.029077,Glycine_max_CO11:0.0):0.014215,(Glycine_max_CO10:0.079794,(Glycine_max_CO6:0.05731,Glycine_max_CO7:0.020694):0.259971):0.018963):0.065158):0.099196):0.029455):0.040714):0.073405,Vitis_vinifera_CO:0.257459):1.0E-6):1.69549):0.144676):0.355539,((((((Ciona_intestinalis_HcI:0.086873,Ciona_intestinalis_HcH:0.026084):0.223948,Ciona_intestinalis_HcG:0.020043):0.133768,(Ciona_intestinalis_HcF:0.074373,Ciona_intestinalis_HcE:0.038911):0.10809):0.28794,(Ciona_intestinalis_HcB:0.102623,(Ciona_intestinalis_HcD:0.017905,Ciona_intestinalis_HcC:0.12415):0.239565):0.043758):0.117051,Ciona_intestinalis_HcA:0.0104):0.439647,(Aplysia_californica_Hc:0.059025,((Megathura_crenulata_Hc:0.277026,Sepia_officinalis_Hc:0.177602):0.162571,Nucula_nucleus_Hc:0.105296):0.058129):0.726573):0.365745):0.264292,Lottia_gigantea_Hc:1.085119):0.211298,Agaricus_bisporus_tyr:0.661946):0.188687,((Neurospora_crassa_tyr2:1.0E-6,Neurospora_tetrasperma_tyr2:0.01927):0.497085,Aspergillus_aculeatus_tyr:0.509398):0.179917):0.210072,(Neurospora_tetrasperma_tyr3:0.009521,Neurospora_crassa_tyr3:1.0E-6):0.453862):0.891258,Neurospora_tetrasperma_tyr1:0.019781,Neurospora_crassa_tyr1:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61717] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_13 = [&R] ((((((((((Candidatus_nitrosopumilus_tyr:0.602183,(Nitrosomonas_europeae_tyr:1.019124,((Bacillus_megaterium_tyr2:0.009149,Bacillus_megaterium_tyr1:3.0E-6):0.209641,Polysphondylium_pallidum_tyr1:0.798115):0.170534):0.133348):0.249221,((Streptomyces_venezuelae_tyr:0.116668,Streptomyces_tsukubaensis_tyr:0.575035):0.316352,(Dictyostelium_discoideum_tyr1:0.016955,Dictyostelium_discoideum_tyr2:0.00929):0.791726):0.067186):0.153798,((((Ectocarpus_siliculosus_tyr1:0.170439,(Ectocarpus_siliculosus_tyr3:0.156589,Ectocarpus_siliculosus_tyr2:0.034149):0.087062):0.148642,((Ectocarpus_siliculosus_tyr5:0.200483,Ectocarpus_siliculosus_tyr6:0.321137):0.50233,Ectocarpus_siliculosus_tyr4:0.258671):0.078503):0.603807,((((((Ectocarpus_siliculosus_tyr18:0.098496,Ectocarpus_siliculosus_tyr16:0.01369):0.02289,Ectocarpus_siliculosus_tyr17:0.118321):0.131125,Ectocarpus_siliculosus_tyr14:0.159245):0.154374,Ectocarpus_siliculosus_tyr15:0.168158):0.387788,(Ectocarpus_siliculosus_tyr13:2.0E-6,Ectocarpus_siliculosus_tyr12:0.201505):0.313548):0.287529,(Ectocarpus_siliculosus_tyr7:0.271386,(((Ectocarpus_siliculosus_tyr11:0.043287,Ectocarpus_siliculosus_tyr10:0.141645):0.072949,Ectocarpus_siliculosus_tyr9:0.046326):0.062047,Ectocarpus_siliculosus_tyr8:0.13453):0.359026):0.331581):0.090561):1.171554,(((Lottia_gigantea_tyr2:1.061318,Pinctada_fucata_tyr1:0.290902):0.135386,((Pinctada_fucata_tyr3:2.0E-6,Pinctada_fucata_tyr2:0.009596):0.141215,Pinctada_fucata_tyr4:0.154447):0.470515):0.136397,((((Phragmatopoma_californica_tyr:0.688173,(((Brugia_malayi_TYR1:0.215878,((((Caenorhabditis_remanei_TYR3:0.067889,Caenorhabditis_briggsae_TYR3:0.0):0.008236,Caenorhabditis_elegans_TYR3:0.020184):0.156044,((Caenorhabditis_elgans_TYR4:0.018964,Caenorhabditis_remanei_TYR4:0.0):0.04502,Caenorhabditis_briggsae_TYR4:0.002599):0.060514):0.176426,(Caenorhabditis_elegans_TYR5:0.051549,Caenorhabditis_briggsae_TYR6:0.047667):0.873871):0.066888):0.017529,(((Brugia_malayi_TYR3:0.31941,(Caenorhabditis_elegans_TYR1:0.0,(Caenorhabditis_remanei_TYR1:0.020253,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.045716):0.047767):0.209666):0.033982,Brugia_malayi_TYR2:0.32871):0.092009,((Caenorhabditis_elegans_TYR2:1.0E-6,(Caenorhabditis_briggsae_TYR2:0.073736,Caenorhabditis_remanei_TYR2:0.005748):0.03465):0.114707,Brugia_malayi_TYR4:0.136147):0.064205):0.162458):0.259211,Caenorhabditis_remanei_TYR5:0.701326):0.096901):0.115696,Lottia_gigantea_tyr1:0.266231):0.135388,((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.118968,Sepia_officinalis_tyr:2.0E-6):0.803595):0.049336,(((Nematostella_vectensis_tyr3:0.299947,Nematostella_vectensis_tyr1:0.889511):0.128165,(Nematostella_vectensis_tyr2:1.04215,Hydra_magnipapillata_tyr:0.471594):0.317415):0.143775,Nematostella_vectensis_tyr4:0.461314):1.278914):0.089181):0.045851):0.259776):0.090351,((((Oryza_sativa_CO:0.260598,(Glycine_max_CO8:0.089143,(Glycine_max_CO9:0.070585,(Glycine_max_CO10:0.190999,(Glycine_max_CO11:0.0,Glycine_max_CO12:0.075312):0.00917):0.089606):0.152519):0.125764):0.03867,((Glycine_max_CO2:0.0,Glycine_max_CO1:0.0):0.136381,((Glycine_max_CO7:0.0,Glycine_max_CO6:0.010626):0.354473,Glycine_max_CO5:0.151971):0.12241):0.094719):0.009601,Vitis_vinifera_CO:0.134969):0.144843,(Glycine_max_CO4:0.033976,Glycine_max_CO3:0.053291):0.134422):1.089171):0.501233,((Lottia_gigantea_Hc:1.53145,(((Ciona_intestinalis_HcE:0.017368,Ciona_intestinalis_HcF:0.094599):0.11829,((Ciona_intestinalis_HcI:0.082934,Ciona_intestinalis_HcH:0.12406):0.113903,Ciona_intestinalis_HcG:0.221308):0.127863):0.284199,((Ciona_intestinalis_HcB:0.092553,(Ciona_intestinalis_HcD:1.0E-6,Ciona_intestinalis_HcC:0.039023):0.139313):0.142371,Ciona_intestinalis_HcA:0.117783):0.09889):0.551875):0.240256,((Aplysia_californica_Hc:0.201887,(Megathura_crenulata_Hc:0.268158,Nucula_nucleus_Hc:0.282338):0.031979):0.078657,Sepia_officinalis_Hc:0.185315):0.303673):0.310339):0.569642,Agaricus_bisporus_tyr:0.511656):0.146013,Aspergillus_aculeatus_tyr:0.729619):0.168555,(Neurospora_tetrasperma_tyr1:0.0,Neurospora_crassa_tyr1:0.0):0.616293):0.101729,(Neurospora_tetrasperma_tyr3:0.027582,Neurospora_crassa_tyr3:0.0):0.379152):0.436385,Neurospora_tetrasperma_tyr2:0.037639,Neurospora_crassa_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61709] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_8 = [&R] ((((((((((Brugia_malayi_TYR2:0.296841,Brugia_malayi_TYR3:0.317843):0.029282,(Brugia_malayi_TYR1:0.159433,((((Caenorhabditis_briggsae_TYR2:0.010045,Caenorhabditis_remanei_TYR2:0.009508):0.009793,Caenorhabditis_elegans_TYR2:0.0):0.057165,Brugia_malayi_TYR4:0.230234):0.175033,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.067076,Caenorhabditis_remanei_TYR1:0.009022):0.02812,Caenorhabditis_elegans_TYR1:1.0E-6):0.089608):0.161856):0.090848):3.0E-6,(Caenorhabditis_remanei_TYR5:0.747043,((Caenorhabditis_briggsae_TYR4:1.0E-6,((Caenorhabditis_remanei_TYR4:0.0,Caenorhabditis_elgans_TYR4:0.0):0.022179,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.039716):0.013906,Caenorhabditis_elegans_TYR3:0.035728):0.29389):0.017172):0.06202,(Caenorhabditis_elegans_TYR5:0.031146,Caenorhabditis_briggsae_TYR6:0.0):1.024659):0.172786):0.086403):0.270373,((((Lottia_gigantea_Hc:0.803649,(((Neurospora_tetrasperma_tyr3:0.019282,Neurospora_crassa_tyr3:1.0E-6):0.260206,((Agaricus_bisporus_tyr:0.73626,(Neurospora_tetrasperma_tyr2:0.039241,Neurospora_crassa_tyr2:0.0):0.275862):0.056842,((Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.009693):0.798758,Aspergillus_aculeatus_tyr:0.473019):0.342754):0.227054):0.22136,((((Oryza_sativa_CO:0.264938,((((Glycine_max_CO12:0.080758,Glycine_max_CO11:0.0):0.0,(Glycine_max_CO10:0.092017,(Glycine_max_CO7:0.021221,Glycine_max_CO6:0.035184):0.169396):0.085213):0.093718,Glycine_max_CO9:0.033794):0.108061,Glycine_max_CO8:0.11156):0.052277):0.089797,Vitis_vinifera_CO:0.1757):1.0E-6,(Glycine_max_CO3:0.063172,Glycine_max_CO4:0.028268):0.291442):0.123811,((Glycine_max_CO2:0.009455,Glycine_max_CO1:0.0):0.199452,Glycine_max_CO5:0.20948):2.0E-6):1.00378):0.152035):0.345319,(((Nucula_nucleus_Hc:0.200755,(Megathura_crenulata_Hc:0.276113,Sepia_officinalis_Hc:0.197039):0.058304):0.116793,Aplysia_californica_Hc:0.056157):0.304236,(((Ciona_intestinalis_HcG:0.375978,(((Ciona_intestinalis_HcH:0.181084,Ciona_intestinalis_HcI:0.050472):0.196837,Ciona_intestinalis_HcE:0.001192):0.046544,Ciona_intestinalis_HcF:0.068843):0.073784):0.440712,(Ciona_intestinalis_HcB:0.131537,(Ciona_intestinalis_HcC:0.113968,Ciona_intestinalis_HcD:0.0):0.181868):9.9E-5):0.33393,Ciona_intestinalis_HcA:8.0E-6):0.674357):0.528808):0.270876,((Nematostella_vectensis_tyr1:0.823683,(Nematostella_vectensis_tyr2:1.46165,(Nematostella_vectensis_tyr4:0.232817,Nematostella_vectensis_tyr3:0.629708):0.189979):0.150625):0.046819,Hydra_magnipapillata_tyr:0.969019):0.824523):0.227649,(((Dictyostelium_discoideum_tyr2:0.009672,Dictyostelium_discoideum_tyr1:0.017875):0.718901,(Streptomyces_venezuelae_tyr:0.11816,Streptomyces_tsukubaensis_tyr:0.399288):0.148912):0.196047,(((Polysphondylium_pallidum_tyr1:0.599172,Nitrosomonas_europeae_tyr:0.825261):0.371216,(Bacillus_megaterium_tyr2:0.0,Bacillus_megaterium_tyr1:0.0):0.219268):0.202638,Candidatus_nitrosopumilus_tyr:0.658758):0.042053):0.206182):0.200144):0.152511,(Lottia_gigantea_tyr1:0.499999,(((((Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.027491):0.152209,Pinctada_fucata_tyr4:0.140042):0.459032,Pinctada_fucata_tyr1:0.572671):0.009368,Lottia_gigantea_tyr2:0.586792):0.262684,Phragmatopoma_californica_tyr:0.446978):0.073629):0.036267):0.191963,((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:1.0E-6):2.0E-6,Sepia_officinalis_tyr:0.084027):0.643913):1.035889,(((Ectocarpus_siliculosus_tyr9:0.047337,(Ectocarpus_siliculosus_tyr11:0.028493,Ectocarpus_siliculosus_tyr10:0.276589):0.130228):0.047713,Ectocarpus_siliculosus_tyr7:0.645424):0.187616,Ectocarpus_siliculosus_tyr8:0.067384):0.49508):0.191206,(((Ectocarpus_siliculosus_tyr6:0.079529,Ectocarpus_siliculosus_tyr5:0.224171):0.36078,Ectocarpus_siliculosus_tyr4:0.319058):0.035652,((Ectocarpus_siliculosus_tyr2:0.027807,Ectocarpus_siliculosus_tyr3:0.104762):0.119231,Ectocarpus_siliculosus_tyr1:0.24466):0.095131):0.53855):0.315165,(Ectocarpus_siliculosus_tyr14:0.093441,(Ectocarpus_siliculosus_tyr18:0.084861,((Ectocarpus_siliculosus_tyr17:0.029562,Ectocarpus_siliculosus_tyr15:0.172893):0.074754,Ectocarpus_siliculosus_tyr16:0.058304):0.049793):0.119011):0.25943):0.405748,Ectocarpus_siliculosus_tyr13:1.0E-6,Ectocarpus_siliculosus_tyr12:0.123166); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61704] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_23 = [&R] (((((((((((((((((Caenorhabditis_briggsae_TYR6:0.0,Caenorhabditis_elegans_TYR5:0.030435):0.899378,((Caenorhabditis_elgans_TYR4:0.027234,Caenorhabditis_remanei_TYR4:0.008706):0.017771,Caenorhabditis_briggsae_TYR4:0.0):1.6E-5):0.196236,((Caenorhabditis_remanei_TYR3:0.045461,Caenorhabditis_briggsae_TYR3:1.0E-6):0.006018,Caenorhabditis_elegans_TYR3:0.029298):0.153759):0.205604,(Brugia_malayi_TYR2:0.43769,Brugia_malayi_TYR3:0.275261):0.036566):0.025631,(((Brugia_malayi_TYR4:0.323416,((Caenorhabditis_elegans_TYR2:0.009497,Caenorhabditis_remanei_TYR2:0.0):0.027557,Caenorhabditis_briggsae_TYR2:0.012312):0.061922):0.123549,((Caenorhabditis_remanei_TYR1:1.0E-6,Caenorhabditis_elegans_TYR1:0.009063):0.036544,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):3.0E-6):0.174679):0.192807,Brugia_malayi_TYR1:0.163879):0.039121):0.147034,Caenorhabditis_remanei_TYR5:0.648236):0.130511,(((((Pinctada_fucata_tyr2:2.0E-6,Pinctada_fucata_tyr3:0.018971):0.188396,Pinctada_fucata_tyr4:0.238507):0.317891,Pinctada_fucata_tyr1:0.612015):0.316224,Lottia_gigantea_tyr2:0.55424):0.161545,(((Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.018862,Sepia_officinalis_tyr:0.046522):0.795652,Lottia_gigantea_tyr1:0.387316):0.247996):0.289749):0.189873,Phragmatopoma_californica_tyr:0.551371):0.078121,(Streptomyces_tsukubaensis_tyr:0.20008,Streptomyces_venezuelae_tyr:0.219306):0.341985):0.063384,((Bacillus_megaterium_tyr1:1.0E-6,Bacillus_megaterium_tyr2:0.032332):0.34152,((Polysphondylium_pallidum_tyr1:0.533549,((Glycine_max_CO4:0.00601,Glycine_max_CO3:0.045571):0.117558,(Glycine_max_CO5:0.364447,(Vitis_vinifera_CO:0.167707,((Glycine_max_CO1:1.0E-6,Glycine_max_CO2:0.009682):0.362015,((Glycine_max_CO8:0.094724,Oryza_sativa_CO:0.151049):0.014988,((((Glycine_max_CO9:0.044846,Glycine_max_CO10:0.101126):0.023808,Glycine_max_CO11:2.0E-6):0.02187,Glycine_max_CO12:0.064407):0.033281,(Glycine_max_CO7:0.010575,Glycine_max_CO6:0.049724):0.253471):0.063429):0.054239):0.041854):0.013252):0.160448):1.098668):0.160013,Nitrosomonas_europeae_tyr:0.702343):0.239945):0.21514):0.066014,Candidatus_nitrosopumilus_tyr:0.75103):0.126596,(((((Agaricus_bisporus_tyr:0.580965,((Aspergillus_aculeatus_tyr:0.590819,(Neurospora_tetrasperma_tyr2:0.0309,Neurospora_crassa_tyr2:1.0E-6):0.343973):0.066684,((Neurospora_tetrasperma_tyr3:0.0,Neurospora_crassa_tyr3:0.0):0.591829,(Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.010037):0.452512):0.277345):0.064535):0.645248,(((Sepia_officinalis_Hc:0.268018,Megathura_crenulata_Hc:0.240601):0.109984,Nucula_nucleus_Hc:0.209194):0.103351,Aplysia_californica_Hc:0.124088):0.414904):0.248682,Lottia_gigantea_Hc:0.872666):0.281893,((((Ciona_intestinalis_HcI:0.252713,Ciona_intestinalis_HcH:4.0E-6):0.238768,Ciona_intestinalis_HcG:0.29822):0.176178,(Ciona_intestinalis_HcE:0.051386,Ciona_intestinalis_HcF:0.107539):0.016434):0.127773,(Ciona_intestinalis_HcA:0.233574,((Ciona_intestinalis_HcD:1.3E-5,Ciona_intestinalis_HcC:0.175191):0.092933,Ciona_intestinalis_HcB:0.142911):0.193672):0.29661):0.438283):0.418134,(Nematostella_vectensis_tyr2:1.191062,((Nematostella_vectensis_tyr4:0.112177,Hydra_magnipapillata_tyr:1.101381):0.169004,(Nematostella_vectensis_tyr3:0.24776,Nematostella_vectensis_tyr1:1.053865):0.191956):0.231223):1.192126):0.458567):0.114402,(Dictyostelium_discoideum_tyr2:0.023132,Dictyostelium_discoideum_tyr1:0.026895):0.497034):1.501665,(((Ectocarpus_siliculosus_tyr9:0.063437,(Ectocarpus_siliculosus_tyr10:0.262079,Ectocarpus_siliculosus_tyr11:0.068421):0.164877):0.111173,Ectocarpus_siliculosus_tyr8:0.205176):0.256924,Ectocarpus_siliculosus_tyr7:0.359947):0.522752):0.23987,(((Ectocarpus_siliculosus_tyr4:0.223025,(Ectocarpus_siliculosus_tyr6:0.312982,Ectocarpus_siliculosus_tyr5:0.305886):0.494066):0.152561,Ectocarpus_siliculosus_tyr1:0.176882):0.224251,(Ectocarpus_siliculosus_tyr2:0.101713,Ectocarpus_siliculosus_tyr3:0.118897):0.014823):0.845648):0.446511,((Ectocarpus_siliculosus_tyr15:0.199184,((Ectocarpus_siliculosus_tyr17:0.077545,Ectocarpus_siliculosus_tyr18:0.170439):0.022436,Ectocarpus_siliculosus_tyr16:0.090549):0.159211):0.175029,Ectocarpus_siliculosus_tyr14:0.12688):0.427224):0.409838,Ectocarpus_siliculosus_tyr12:0.183373,Ectocarpus_siliculosus_tyr13:2.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61719] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_1 = [&R] (((((((((Sepia_officinalis_tyr:0.066741,(Illex_argentinus_tyr1:0.0,Illex_argentinus_tyr2:0.0):0.044539):1.065941,((((Nitrosomonas_europeae_tyr:1.136173,Polysphondylium_pallidum_tyr1:0.48675):0.143503,(Candidatus_nitrosopumilus_tyr:0.442067,(Bacillus_megaterium_tyr2:0.009062,Bacillus_megaterium_tyr1:1.0E-6):0.167607):0.229804):0.35427,(Dictyostelium_discoideum_tyr2:0.0,Dictyostelium_discoideum_tyr1:0.0):0.453396):0.313962,(Streptomyces_venezuelae_tyr:0.144429,Streptomyces_tsukubaensis_tyr:0.473827):0.319186):0.148894):0.093193,((((Nematostella_vectensis_tyr4:0.550595,Nematostella_vectensis_tyr3:0.442081):0.190254,Nematostella_vectensis_tyr2:0.721929):0.086815,Hydra_magnipapillata_tyr:0.761034):0.254978,Nematostella_vectensis_tyr1:0.519213):0.365044):3.0E-6,(((Brugia_malayi_TYR1:0.324208,(((Caenorhabditis_elegans_TYR2:0.010396,Caenorhabditis_remanei_TYR2:0.008637):0.031516,Caenorhabditis_briggsae_TYR2:0.033256):0.207505,Brugia_malayi_TYR4:0.181773):0.045705):0.02422,(((Brugia_malayi_TYR3:0.177426,((Caenorhabditis_remanei_TYR1:1.0E-6,Caenorhabditis_elegans_TYR1:0.01632):0.033825,(Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):1.0E-6):0.251697):0.12191,(((Caenorhabditis_briggsae_TYR3:1.0E-6,Caenorhabditis_elegans_TYR3:0.009253):0.004131,Caenorhabditis_remanei_TYR3:0.024312):0.150417,(Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_remanei_TYR4:0.017684,Caenorhabditis_elgans_TYR4:0.018894):0.094602):0.089087):0.202329):0.060269,((Caenorhabditis_elegans_TYR5:2.0E-6,Caenorhabditis_briggsae_TYR6:0.036064):0.872374,Brugia_malayi_TYR2:0.276689):0.061857):0.033522):0.579781,(((Pinctada_fucata_tyr4:0.217582,(Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.018821):0.230703):0.748752,Pinctada_fucata_tyr1:0.284341):0.364908,((Phragmatopoma_californica_tyr:0.705487,Lottia_gigantea_tyr1:0.581431):0.190575,(Caenorhabditis_remanei_TYR5:0.626311,Lottia_gigantea_tyr2:0.685062):0.046139):0.237031):0.101729):0.083316):0.164031,((((((Vitis_vinifera_CO:0.198138,Oryza_sativa_CO:0.187471):0.066963,(Glycine_max_CO8:0.055791,(((Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.028215):0.033661,(Glycine_max_CO10:0.152976,(Glycine_max_CO7:0.020259,Glycine_max_CO6:0.0):0.277129):0.097853):0.097259,Glycine_max_CO9:0.027834):0.201852):0.098278):0.055462,Glycine_max_CO5:0.280649):0.064032,(Glycine_max_CO2:0.0,Glycine_max_CO1:0.0):0.123531):0.017569,(Glycine_max_CO3:0.056837,Glycine_max_CO4:0.025651):0.366978):0.567412,((Lottia_gigantea_Hc:0.772816,((((Nucula_nucleus_Hc:0.189788,Megathura_crenulata_Hc:0.395546):0.088201,Aplysia_californica_Hc:0.207145):0.088037,Sepia_officinalis_Hc:0.105983):0.332248,(((Ciona_intestinalis_HcD:0.0,Ciona_intestinalis_HcC:0.065937):0.234458,(((Ciona_intestinalis_HcI:0.042684,(Ciona_intestinalis_HcE:1.0E-6,Ciona_intestinalis_HcF:0.074907):0.117216):0.007219,(Ciona_intestinalis_HcG:0.213945,Ciona_intestinalis_HcH:1.0E-6):0.056005):0.290839,Ciona_intestinalis_HcB:5.0E-6):0.078493):4.6E-5,Ciona_intestinalis_HcA:0.069607):0.575729):0.297868):0.150098,(Agaricus_bisporus_tyr:0.394624,((((Neurospora_tetrasperma_tyr2:0.0,Neurospora_crassa_tyr2:1.0E-6):0.356723,(Neurospora_tetrasperma_tyr3:0.01771,Neurospora_crassa_tyr3:1.0E-6):0.383001):0.099446,(Neurospora_tetrasperma_tyr1:0.018791,Neurospora_crassa_tyr1:1.0E-6):0.712324):0.075732,Aspergillus_aculeatus_tyr:0.469777):0.017902):0.961461):0.683088):0.30658):1.00237,((Ectocarpus_siliculosus_tyr8:0.088721,((Ectocarpus_siliculosus_tyr9:0.061164,Ectocarpus_siliculosus_tyr11:1.0E-6):0.010159,Ectocarpus_siliculosus_tyr10:0.185352):0.071114):0.220535,Ectocarpus_siliculosus_tyr7:0.40778):3.0E-5):0.497003,(((Ectocarpus_siliculosus_tyr6:0.270501,Ectocarpus_siliculosus_tyr5:0.364046):0.146519,Ectocarpus_siliculosus_tyr4:0.292724):0.075731,(Ectocarpus_siliculosus_tyr1:0.183206,(Ectocarpus_siliculosus_tyr3:0.126738,Ectocarpus_siliculosus_tyr2:0.015039):0.112258):1.0E-6):0.661438):0.202001,(Ectocarpus_siliculosus_tyr15:0.173153,((Ectocarpus_siliculosus_tyr17:0.122798,(Ectocarpus_siliculosus_tyr16:0.050688,Ectocarpus_siliculosus_tyr18:0.037499):0.048972):0.134998,Ectocarpus_siliculosus_tyr14:0.226322):0.171321):0.37033):0.458139,Ectocarpus_siliculosus_tyr12:0.114297,Ectocarpus_siliculosus_tyr13:3.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61697] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_25 = [&R] (((((((((((((Brugia_malayi_TYR3:0.17983,((((Caenorhabditis_briggsae_TYR2:0.017114,Caenorhabditis_remanei_TYR2:0.015125):0.02633,Caenorhabditis_elegans_TYR2:1.0E-6):0.039464,Brugia_malayi_TYR4:0.249398):0.090861,(((Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.007837,Caenorhabditis_remanei_TYR1:0.0):0.032297,Caenorhabditis_elegans_TYR1:0.0):0.091574):0.114924):0.012889,Brugia_malayi_TYR2:0.332085):0.032237,((((Caenorhabditis_elegans_TYR5:0.023479,Caenorhabditis_briggsae_TYR6:1.0E-6):0.973218,(Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_remanei_TYR4:1.0E-6,Caenorhabditis_elgans_TYR4:0.023084):0.068861):3.0E-6):0.076859,(Caenorhabditis_remanei_TYR3:0.028438,(Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_elegans_TYR3:0.015376):0.019187):0.114781):0.122438,Brugia_malayi_TYR1:0.046891):0.028068):0.089236,(((((((Pinctada_fucata_tyr2:1.0E-6,Pinctada_fucata_tyr3:0.023449):0.191773,Pinctada_fucata_tyr4:0.101525):0.495391,Lottia_gigantea_tyr2:0.565641):0.085533,Pinctada_fucata_tyr1:0.67748):0.405775,Lottia_gigantea_tyr1:0.078788):0.056811,(Sepia_officinalis_tyr:0.101857,(Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.008503):0.376073):0.431139,Caenorhabditis_remanei_TYR5:0.506382):0.254695):0.119563,((((Hydra_magnipapillata_tyr:0.733463,Nematostella_vectensis_tyr2:0.74732):0.284112,Nematostella_vectensis_tyr1:0.690191):0.12314,(Nematostella_vectensis_tyr3:0.101705,Nematostella_vectensis_tyr4:0.44066):0.144736):0.637139,(Streptomyces_venezuelae_tyr:2.0E-6,Streptomyces_tsukubaensis_tyr:0.513191):0.191606):0.172445):0.311912,(Dictyostelium_discoideum_tyr2:0.007554,Dictyostelium_discoideum_tyr1:0.0):0.509101):0.191279,((Bacillus_megaterium_tyr2:0.026781,Bacillus_megaterium_tyr1:1.0E-6):0.3518,(Phragmatopoma_californica_tyr:0.487341,Candidatus_nitrosopumilus_tyr:0.516942):0.02652):0.125079):0.039176,(Nitrosomonas_europeae_tyr:0.467609,Polysphondylium_pallidum_tyr1:0.495924):0.078032):0.311081,((((Ectocarpus_siliculosus_tyr10:0.104063,Ectocarpus_siliculosus_tyr11:0.010719):0.014304,(Ectocarpus_siliculosus_tyr8:0.155183,Ectocarpus_siliculosus_tyr9:0.052259):0.029707):0.170177,Ectocarpus_siliculosus_tyr7:0.182113):0.252933,((((Ectocarpus_siliculosus_tyr5:0.193165,Ectocarpus_siliculosus_tyr6:0.318668):0.221122,Ectocarpus_siliculosus_tyr4:0.210099):0.040023,(Ectocarpus_siliculosus_tyr1:0.140367,(Ectocarpus_siliculosus_tyr2:0.077729,Ectocarpus_siliculosus_tyr3:0.060386):0.130267):0.036976):0.382676,((((Ectocarpus_siliculosus_tyr16:0.075829,(Ectocarpus_siliculosus_tyr17:0.024078,Ectocarpus_siliculosus_tyr18:0.153878):0.018297):0.048402,Ectocarpus_siliculosus_tyr15:0.204008):0.187558,Ectocarpus_siliculosus_tyr14:0.062206):0.205232,(Ectocarpus_siliculosus_tyr12:0.111955,Ectocarpus_siliculosus_tyr13:0.003677):0.32839):0.184464):0.273184):0.847449):0.521896,(Lottia_gigantea_Hc:0.653069,(((((Ciona_intestinalis_HcF:0.051446,Ciona_intestinalis_HcE:0.016319):0.066003,(Ciona_intestinalis_HcG:0.11838,(Ciona_intestinalis_HcH:0.020444,Ciona_intestinalis_HcI:0.059434):0.040545):0.027619):0.243101,((Ciona_intestinalis_HcB:0.056319,(Ciona_intestinalis_HcC:0.07952,Ciona_intestinalis_HcD:1.0E-6):0.088367):0.087572,Ciona_intestinalis_HcA:4.0E-6):0.160424):0.385305,(((Nucula_nucleus_Hc:0.195403,Megathura_crenulata_Hc:0.110881):0.070538,Aplysia_californica_Hc:0.088217):0.056841,Sepia_officinalis_Hc:0.085614):0.481823):0.371256,(((((((Glycine_max_CO9:0.032114,((Glycine_max_CO11:0.0,Glycine_max_CO12:0.017243):1.0E-6,((Glycine_max_CO6:0.008401,Glycine_max_CO7:0.009327):0.116785,Glycine_max_CO10:0.066804):0.037538):0.052181):0.072716,Glycine_max_CO8:0.076969):0.020113,Oryza_sativa_CO:0.13466):0.031976,(Glycine_max_CO1:0.0,Glycine_max_CO2:0.008177):0.112211):0.04696,Glycine_max_CO5:0.166632):6.0E-6,Vitis_vinifera_CO:0.238033):0.115617,(Glycine_max_CO3:0.058814,Glycine_max_CO4:0.035293):0.163618):1.379369):0.103929):0.190245):0.456418,(((Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.008613):0.589083,Agaricus_bisporus_tyr:0.425663):0.120953,(Neurospora_crassa_tyr3:1.0E-6,Neurospora_tetrasperma_tyr3:0.025118):0.372922):0.092385):0.211305,Aspergillus_aculeatus_tyr:0.477299):0.441698,Neurospora_tetrasperma_tyr2:0.008155,Neurospora_crassa_tyr2:0.0); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61721] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_10 = [&R] ((((((((((((((((((Caenorhabditis_elegans_TYR1:0.008439,Caenorhabditis_remanei_TYR1:0.008349):0.025385,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):1.0E-6):0.204642,(Caenorhabditis_briggsae_TYR2:0.01972,(Caenorhabditis_elegans_TYR2:0.009027,Caenorhabditis_remanei_TYR2:1.0E-6):0.018682):0.06178):0.102363,Brugia_malayi_TYR4:0.183602):0.093239,(((((Caenorhabditis_elegans_TYR3:0.0,Caenorhabditis_briggsae_TYR3:0.0):1.0E-6,Caenorhabditis_remanei_TYR3:0.027355):0.228484,((Caenorhabditis_elegans_TYR5:1.0E-6,Caenorhabditis_briggsae_TYR6:0.026254):0.933915,((Caenorhabditis_elgans_TYR4:0.027079,Caenorhabditis_remanei_TYR4:0.008304):0.044448,Caenorhabditis_briggsae_TYR4:1.0E-6):0.005895):0.134853):0.061043,Brugia_malayi_TYR1:0.228093):0.042425,Brugia_malayi_TYR2:0.397304):0.062885):0.024348,Brugia_malayi_TYR3:0.313613):0.072324,(Nematostella_vectensis_tyr1:0.435607,(Nematostella_vectensis_tyr4:0.376492,((Hydra_magnipapillata_tyr:0.840272,Nematostella_vectensis_tyr2:0.857128):0.383747,Nematostella_vectensis_tyr3:0.190967):0.114309):0.420048):0.646941):0.133019,(((((Nitrosomonas_europeae_tyr:0.898177,Polysphondylium_pallidum_tyr1:0.320481):0.196147,(Bacillus_megaterium_tyr1:2.0E-6,Bacillus_megaterium_tyr2:0.009317):0.263086):0.132828,Candidatus_nitrosopumilus_tyr:0.426027):0.148256,(Streptomyces_tsukubaensis_tyr:0.430519,Streptomyces_venezuelae_tyr:0.073519):0.304624):0.042944,(((((Ectocarpus_siliculosus_tyr15:0.267663,((Ectocarpus_siliculosus_tyr17:0.081534,Ectocarpus_siliculosus_tyr18:0.074798):0.030317,Ectocarpus_siliculosus_tyr16:0.050782):0.069235):0.144064,Ectocarpus_siliculosus_tyr14:0.047887):0.517156,(Ectocarpus_siliculosus_tyr12:0.164247,Ectocarpus_siliculosus_tyr13:6.0E-6):0.552696):0.235848,(((Ectocarpus_siliculosus_tyr6:0.136682,Ectocarpus_siliculosus_tyr5:0.442031):0.222625,(((Ectocarpus_siliculosus_tyr2:0.051538,Ectocarpus_siliculosus_tyr3:0.118864):0.187954,Ectocarpus_siliculosus_tyr1:0.110769):0.119928,Ectocarpus_siliculosus_tyr4:0.35405):0.133086):0.39345,((((Ectocarpus_siliculosus_tyr8:0.316682,Ectocarpus_siliculosus_tyr9:0.05596):0.032384,Ectocarpus_siliculosus_tyr11:2.0E-6):0.065914,Ectocarpus_siliculosus_tyr10:0.106799):0.158477,Ectocarpus_siliculosus_tyr7:0.241595):0.367996):0.190262):0.853897,(((((Pinctada_fucata_tyr3:0.028375,Pinctada_fucata_tyr2:5.0E-6):0.186418,Pinctada_fucata_tyr4:0.124202):0.509931,Phragmatopoma_californica_tyr:0.281606):0.065358,(Dictyostelium_discoideum_tyr2:0.0,Dictyostelium_discoideum_tyr1:0.0):0.631899):0.034031,Caenorhabditis_remanei_TYR5:0.813792):0.18104):0.071449):0.176381):0.307793,(Lottia_gigantea_tyr1:0.48478,((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.048326,Sepia_officinalis_tyr:0.022593):0.435051):0.347806):0.060486,(Lottia_gigantea_tyr2:0.509998,Pinctada_fucata_tyr1:0.712789):0.028098):0.416167,(Glycine_max_CO5:0.169802,(((Glycine_max_CO8:0.157785,Oryza_sativa_CO:0.208526):0.031258,((Glycine_max_CO9:0.048857,((Glycine_max_CO12:0.026955,Glycine_max_CO11:1.0E-6):0.004873,Glycine_max_CO10:0.149355):0.08018):0.082386,((Glycine_max_CO1:0.0,Glycine_max_CO2:0.017381):0.143655,(Glycine_max_CO6:0.022028,Glycine_max_CO7:0.052478):0.283783):0.019062):0.040885):0.029825,(Vitis_vinifera_CO:0.35695,(Glycine_max_CO4:0.042894,Glycine_max_CO3:0.044171):0.27611):0.033059):0.006638):1.049079):0.270777,(((Neurospora_tetrasperma_tyr3:0.00853,Neurospora_crassa_tyr3:1.0E-6):0.499219,((Aspergillus_aculeatus_tyr:0.489947,(Neurospora_tetrasperma_tyr2:0.0,Neurospora_crassa_tyr2:0.0):0.371687):0.080672,(Neurospora_crassa_tyr1:1.0E-6,Neurospora_tetrasperma_tyr1:0.018696):0.475962):0.137461):0.215987,Agaricus_bisporus_tyr:0.349922):0.257797):0.546011,Lottia_gigantea_Hc:0.361586):0.503785,(((Megathura_crenulata_Hc:0.309602,Sepia_officinalis_Hc:0.119695):0.09856,Nucula_nucleus_Hc:0.146565):0.049353,Aplysia_californica_Hc:0.212917):0.608581):0.396362,Ciona_intestinalis_HcA:3.0E-6):0.1618,(Ciona_intestinalis_HcB:0.112637,(Ciona_intestinalis_HcD:0.005445,Ciona_intestinalis_HcC:0.129575):0.233017):0.032247):0.311775,((Ciona_intestinalis_HcI:0.11776,Ciona_intestinalis_HcH:1.0E-6):0.110682,Ciona_intestinalis_HcG:0.039764):0.029024):0.169007,Ciona_intestinalis_HcE:0.036834,Ciona_intestinalis_HcF:0.106145); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61706] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_4 = [&R] ((((((((((((((((Caenorhabditis_remanei_TYR3:2.0E-6,(Caenorhabditis_elegans_TYR3:0.023895,Caenorhabditis_briggsae_TYR3:1.0E-6):0.015766):0.114817,(Caenorhabditis_briggsae_TYR4:0.0,(Caenorhabditis_elgans_TYR4:0.015422,Caenorhabditis_remanei_TYR4:0.014766):0.045889):0.049513):0.077839,Brugia_malayi_TYR1:0.156387):0.03052,(((((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):0.021555,Caenorhabditis_remanei_TYR1:0.010622):0.023214,Caenorhabditis_elegans_TYR1:1.0E-6):0.105149,(((Caenorhabditis_remanei_TYR2:0.005421,Caenorhabditis_briggsae_TYR2:0.05919):0.029151,Caenorhabditis_elegans_TYR2:1.0E-6):0.113545,Brugia_malayi_TYR4:0.176428):0.077778):0.042356,Brugia_malayi_TYR2:0.27046):0.057556):0.03206,(Brugia_malayi_TYR3:0.158072,(Caenorhabditis_briggsae_TYR6:0.0,Caenorhabditis_elegans_TYR5:0.03455):0.679509):0.027972):0.168302,Caenorhabditis_remanei_TYR5:0.601813):0.116607,((((Dictyostelium_discoideum_tyr2:0.031532,Dictyostelium_discoideum_tyr1:1.0E-6):0.342304,Candidatus_nitrosopumilus_tyr:0.525567):0.345785,((Streptomyces_tsukubaensis_tyr:0.638082,Streptomyces_venezuelae_tyr:0.021491):0.247535,(((Nematostella_vectensis_tyr4:0.428309,Nematostella_vectensis_tyr3:0.205795):0.039943,Nematostella_vectensis_tyr1:0.665072):3.0E-6,(Nematostella_vectensis_tyr2:0.844509,Hydra_magnipapillata_tyr:0.338715):0.486744):0.615957):0.056297):0.11117,(Polysphondylium_pallidum_tyr1:0.504395,((Bacillus_megaterium_tyr2:0.008038,Bacillus_megaterium_tyr1:1.0E-6):0.395433,Nitrosomonas_europeae_tyr:0.728481):6.9E-5):0.107583):0.254852):0.139179,(((Ectocarpus_siliculosus_tyr4:0.190671,(Ectocarpus_siliculosus_tyr6:0.222043,Ectocarpus_siliculosus_tyr5:0.192411):0.314739):0.045315,((Ectocarpus_siliculosus_tyr3:0.063966,Ectocarpus_siliculosus_tyr2:0.040658):0.229352,Ectocarpus_siliculosus_tyr1:0.08574):0.092287):0.573996,(((Ectocarpus_siliculosus_tyr14:0.031325,(Ectocarpus_siliculosus_tyr15:0.20529,((Ectocarpus_siliculosus_tyr17:0.045944,Ectocarpus_siliculosus_tyr18:0.12172):0.069067,Ectocarpus_siliculosus_tyr16:0.09098):0.042368):0.224043):0.393982,(Ectocarpus_siliculosus_tyr12:0.139855,Ectocarpus_siliculosus_tyr13:2.0E-6):0.389947):0.190493,((((Ectocarpus_siliculosus_tyr10:0.107949,Ectocarpus_siliculosus_tyr11:0.00875):0.021487,Ectocarpus_siliculosus_tyr9:0.04845):0.004508,Ectocarpus_siliculosus_tyr8:0.164176):0.156021,Ectocarpus_siliculosus_tyr7:0.290593):0.328095):0.136948):0.518433):0.242459,(((Lottia_gigantea_tyr2:0.735705,(Pinctada_fucata_tyr1:0.551766,(Pinctada_fucata_tyr4:0.157003,(Pinctada_fucata_tyr2:0.0,Pinctada_fucata_tyr3:0.008392):0.298415):0.361855):0.168432):0.104229,Phragmatopoma_californica_tyr:0.655316):0.137987,(((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.025134,Sepia_officinalis_tyr:0.123295):0.491356,Lottia_gigantea_tyr1:0.191234):0.214031):0.135448):0.324059,(((Glycine_max_CO3:0.02558,Glycine_max_CO4:0.016068):0.170972,Vitis_vinifera_CO:0.181534):4.0E-6,((((((Glycine_max_CO10:0.100526,(Glycine_max_CO12:0.024289,Glycine_max_CO11:1.0E-6):0.024689):0.048652,Glycine_max_CO9:0.025121):0.032732,Glycine_max_CO8:0.111772):0.022472,((Glycine_max_CO7:0.0,Glycine_max_CO6:0.0):0.115599,Glycine_max_CO5:0.240418):0.129997):0.00713,Oryza_sativa_CO:0.140661):0.027296,(Glycine_max_CO1:1.0E-6,Glycine_max_CO2:0.016161):0.152995):0.091395):1.517988):0.243018,((((Ciona_intestinalis_HcD:2.0E-6,(((Ciona_intestinalis_HcE:0.012485,Ciona_intestinalis_HcF:0.042892):0.014462,Ciona_intestinalis_HcG:0.092626):1.0E-6,(Ciona_intestinalis_HcH:0.022624,Ciona_intestinalis_HcI:0.071115):0.055141):0.611986):0.07203,((Ciona_intestinalis_HcC:4.0E-6,Ciona_intestinalis_HcB:0.133082):0.026442,Ciona_intestinalis_HcA:1.5E-5):0.056121):0.580499,(((Sepia_officinalis_Hc:0.065619,Megathura_crenulata_Hc:0.281535):0.081891,Nucula_nucleus_Hc:0.194572):0.108142,Aplysia_californica_Hc:0.082927):0.669921):0.488966,Lottia_gigantea_Hc:0.614778):0.293925):0.505198,Aspergillus_aculeatus_tyr:0.484053):0.195771,(Neurospora_tetrasperma_tyr2:0.016164,Neurospora_crassa_tyr2:0.0):0.39203):0.152481,(Neurospora_tetrasperma_tyr3:0.0,Neurospora_crassa_tyr3:0.0):0.331753):0.280721,Agaricus_bisporus_tyr:0.562412):0.591337,Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.00881); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61700] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_3 = [&R] (((((((((((((((((Brugia_malayi_TYR1:0.111013,((((((Caenorhabditis_remanei_TYR2:0.007321,Caenorhabditis_elegans_TYR2:0.016471):0.016544,Caenorhabditis_briggsae_TYR2:0.008871):0.029702,((Caenorhabditis_remanei_TYR1:0.00726,Caenorhabditis_elegans_TYR1:1.0E-6):0.014635,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):1.0E-6):0.308445):0.101899,Brugia_malayi_TYR4:0.135742):0.098011,Brugia_malayi_TYR3:0.327267):0.043188,Brugia_malayi_TYR2:0.344934):0.074376):2.0E-6,((Caenorhabditis_briggsae_TYR4:1.0E-6,(Caenorhabditis_remanei_TYR4:0.007447,Caenorhabditis_elgans_TYR4:0.015473):0.022904):0.113487,(Caenorhabditis_remanei_TYR3:0.020253,(Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_elegans_TYR3:0.007742):0.01231):0.239692):0.141848):0.086043,(Caenorhabditis_briggsae_TYR6:0.031344,Caenorhabditis_elegans_TYR5:1.0E-6):0.565827):0.109295,Caenorhabditis_remanei_TYR5:0.725498):0.157355,((((((Dictyostelium_discoideum_tyr2:0.015066,Dictyostelium_discoideum_tyr1:0.0):0.782987,Phragmatopoma_californica_tyr:0.35286):0.209993,(Pinctada_fucata_tyr4:0.137413,(Pinctada_fucata_tyr2:6.0E-6,Pinctada_fucata_tyr3:0.025227):0.218875):0.411006):0.22274,Pinctada_fucata_tyr1:0.331551):0.154747,Lottia_gigantea_tyr2:0.627421):0.065975,(((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):2.3E-5,Sepia_officinalis_tyr:0.083752):0.642483,Lottia_gigantea_tyr1:0.384432):0.081539):0.105987):0.12691,(((Nematostella_vectensis_tyr3:0.473025,(Nematostella_vectensis_tyr4:0.324746,Hydra_magnipapillata_tyr:0.763986):0.156387):0.071425,Nematostella_vectensis_tyr2:0.851023):0.105338,Nematostella_vectensis_tyr1:0.940362):0.657981):0.147347,(((((Glycine_max_CO5:0.18542,(Glycine_max_CO6:0.009089,Glycine_max_CO7:0.018514):0.237852):0.102374,(Glycine_max_CO2:0.016813,Glycine_max_CO1:1.0E-6):0.120894):0.079367,(((Glycine_max_CO9:0.028789,((Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.02472):0.027344,Glycine_max_CO10:0.127999):0.039074):0.032765,Glycine_max_CO8:0.103401):0.067039,Oryza_sativa_CO:0.205063):0.01376):0.07283,Vitis_vinifera_CO:0.137517):0.094444,(Glycine_max_CO3:0.060388,Glycine_max_CO4:0.036825):0.151119):1.321957):2.4E-5,(Candidatus_nitrosopumilus_tyr:0.398782,(((Polysphondylium_pallidum_tyr1:0.653131,Nitrosomonas_europeae_tyr:0.651112):0.230269,(Bacillus_megaterium_tyr1:3.0E-6,Bacillus_megaterium_tyr2:0.016797):0.361252):0.13198,(Streptomyces_tsukubaensis_tyr:0.356194,Streptomyces_venezuelae_tyr:0.065966):0.291765):0.104574):0.064298):0.23488,(((Ectocarpus_siliculosus_tyr12:0.130062,Ectocarpus_siliculosus_tyr13:2.0E-6):0.213693,((((Ectocarpus_siliculosus_tyr2:0.05959,Ectocarpus_siliculosus_tyr3:0.058349):0.155301,Ectocarpus_siliculosus_tyr1:0.151427):0.061464,((Ectocarpus_siliculosus_tyr5:0.257883,Ectocarpus_siliculosus_tyr6:0.301701):0.285343,Ectocarpus_siliculosus_tyr4:0.363449):0.043303):0.667082,(((Ectocarpus_siliculosus_tyr11:9.0E-6,(Ectocarpus_siliculosus_tyr9:0.070281,Ectocarpus_siliculosus_tyr10:0.087319):0.04243):0.09448,Ectocarpus_siliculosus_tyr8:0.188525):0.090603,Ectocarpus_siliculosus_tyr7:0.233104):0.27507):0.198532):0.129125,(((Ectocarpus_siliculosus_tyr17:0.048331,(Ectocarpus_siliculosus_tyr18:0.094203,Ectocarpus_siliculosus_tyr16:0.074761):0.055428):0.112284,Ectocarpus_siliculosus_tyr15:0.19635):0.095634,Ectocarpus_siliculosus_tyr14:0.122795):0.239092):0.873759):0.216967,Lottia_gigantea_Hc:0.642179):0.221408,((((Ciona_intestinalis_HcB:0.088073,Ciona_intestinalis_HcC:0.111537):0.036792,Ciona_intestinalis_HcD:0.022388):0.116449,Ciona_intestinalis_HcA:0.013898):0.069189,((Ciona_intestinalis_HcE:0.050445,Ciona_intestinalis_HcF:0.06594):0.062631,(Ciona_intestinalis_HcG:0.055973,(Ciona_intestinalis_HcI:0.131043,Ciona_intestinalis_HcH:0.054475):0.084028):0.045158):0.296244):0.438279):0.081778,(Sepia_officinalis_Hc:0.139964,((Nucula_nucleus_Hc:0.23168,Megathura_crenulata_Hc:0.202597):0.030276,Aplysia_californica_Hc:0.166812):0.175568):0.381029):0.569136,Agaricus_bisporus_tyr:0.621405):0.115144,(Neurospora_tetrasperma_tyr1:0.02621,Neurospora_crassa_tyr1:1.0E-6):0.548164):0.16086,Aspergillus_aculeatus_tyr:0.678024):0.271071,(Neurospora_tetrasperma_tyr3:0.0,Neurospora_crassa_tyr3:0.0):0.304991):0.420058,Neurospora_tetrasperma_tyr2:0.015805,Neurospora_crassa_tyr2:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61699] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_9 = [&R] (((((((((((((((((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.093657):0.023864,Caenorhabditis_elegans_TYR3:0.008392):0.173514,(Caenorhabditis_briggsae_TYR4:8.47E-4,(Caenorhabditis_elgans_TYR4:0.007842,Caenorhabditis_remanei_TYR4:0.0):0.03069):0.083287):0.134752,Brugia_malayi_TYR2:0.398071):2.0E-6,Brugia_malayi_TYR1:0.175484):0.050512,(((Brugia_malayi_TYR4:0.152328,((Caenorhabditis_elegans_TYR2:0.016871,Caenorhabditis_remanei_TYR2:0.007479):0.017206,Caenorhabditis_briggsae_TYR2:0.00885):0.036988):0.113828,(Caenorhabditis_elegans_TYR1:1.0E-6,((Caenorhabditis_briggsae_TYR5:0.0,Caenorhabditis_briggsae_TYR1:0.0):1.0E-6,Caenorhabditis_remanei_TYR1:0.015727):0.015809):0.06999):0.164596,Brugia_malayi_TYR3:0.283461):0.06827):0.007472,(Caenorhabditis_elegans_TYR5:0.034368,Caenorhabditis_briggsae_TYR6:0.0):0.795105):0.198203,((((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.001064,Sepia_officinalis_tyr:0.092561):0.514631,Lottia_gigantea_tyr1:0.245806):0.15176,(((Pinctada_fucata_tyr3:0.018407,Pinctada_fucata_tyr2:0.021507):0.145971,Pinctada_fucata_tyr4:0.209241):0.208976,Pinctada_fucata_tyr1:0.398866):0.192882):0.185233):0.209437,(Caenorhabditis_remanei_TYR5:0.463464,(Phragmatopoma_californica_tyr:0.227707,((((Ectocarpus_siliculosus_tyr12:0.08964,Ectocarpus_siliculosus_tyr13:1.0E-6):0.211435,((((Ectocarpus_siliculosus_tyr18:0.107792,Ectocarpus_siliculosus_tyr16:0.011231):0.011304,Ectocarpus_siliculosus_tyr17:0.036398):0.097976,Ectocarpus_siliculosus_tyr15:0.164553):0.162948,Ectocarpus_siliculosus_tyr14:0.054883):0.372981):0.267929,(((Ectocarpus_siliculosus_tyr9:0.081221,Ectocarpus_siliculosus_tyr8:0.104158):0.028893,(Ectocarpus_siliculosus_tyr10:0.10976,Ectocarpus_siliculosus_tyr11:0.025389):0.0495):0.121929,Ectocarpus_siliculosus_tyr7:0.19369):0.409447):0.28879,((((Ectocarpus_siliculosus_tyr2:0.034987,Ectocarpus_siliculosus_tyr3:0.150684):0.125291,Ectocarpus_siliculosus_tyr1:0.149962):0.065035,Ectocarpus_siliculosus_tyr4:0.390725):0.043117,(Ectocarpus_siliculosus_tyr6:0.225762,Ectocarpus_siliculosus_tyr5:0.359973):0.281943):0.251281):0.684357):0.02578):0.133872):0.076621,Lottia_gigantea_tyr2:1.184118):0.198769,((((Bacillus_megaterium_tyr1:0.0,Bacillus_megaterium_tyr2:0.0):0.227666,Nitrosomonas_europeae_tyr:0.443859):0.052567,Polysphondylium_pallidum_tyr1:0.33676):0.117573,((Dictyostelium_discoideum_tyr1:0.0,Dictyostelium_discoideum_tyr2:0.0):0.482369,Candidatus_nitrosopumilus_tyr:0.511046):0.138223):3.0E-6):0.150412,(Streptomyces_tsukubaensis_tyr:0.317336,(Streptomyces_venezuelae_tyr:0.204476,(Hydra_magnipapillata_tyr:0.641105,((Nematostella_vectensis_tyr1:0.942795,Nematostella_vectensis_tyr2:0.989355):0.328349,(Nematostella_vectensis_tyr3:0.348279,Nematostella_vectensis_tyr4:0.386915):0.181535):0.149734):0.323809):0.067835):0.133552):0.452144,(((((((Oryza_sativa_CO:0.168922,Glycine_max_CO8:0.124392):0.043044,(((Glycine_max_CO6:0.0,Glycine_max_CO7:0.0):0.086134,((Glycine_max_CO9:0.103012,(Glycine_max_CO11:1.0E-6,Glycine_max_CO12:0.026476):1.0E-6):0.019765,Glycine_max_CO10:0.091473):0.035502):0.059595,(Glycine_max_CO2:0.008338,Glycine_max_CO1:0.0):0.159085):0.028717):0.065849,Vitis_vinifera_CO:0.084184):0.040547,Glycine_max_CO5:0.209218):0.131074,(Glycine_max_CO3:0.030426,Glycine_max_CO4:0.026281):0.052268):1.006298,Lottia_gigantea_Hc:0.434144):0.307433,(((Ciona_intestinalis_HcA:3.0E-6,((Ciona_intestinalis_HcB:0.073924,Ciona_intestinalis_HcC:0.089207):0.056793,Ciona_intestinalis_HcD:0.013477):0.080226):0.137065,(Ciona_intestinalis_HcF:0.124413,(Ciona_intestinalis_HcE:3.0E-6,((Ciona_intestinalis_HcH:0.058457,Ciona_intestinalis_HcG:0.371339):0.143842,Ciona_intestinalis_HcI:0.045403):0.299631):0.013311):0.33513):0.380414,(((Aplysia_californica_Hc:0.129034,Megathura_crenulata_Hc:0.150363):0.094556,Nucula_nucleus_Hc:0.219257):0.09925,Sepia_officinalis_Hc:0.094466):0.442344):0.294556):0.194093):0.408891,Agaricus_bisporus_tyr:0.515146):0.094311,(Neurospora_tetrasperma_tyr3:0.015847,Neurospora_crassa_tyr3:1.0E-6):0.411105):0.222156,((Neurospora_crassa_tyr1:0.0,Neurospora_tetrasperma_tyr1:0.0):0.497985,Aspergillus_aculeatus_tyr:0.360461):0.113952):0.466825,Neurospora_crassa_tyr2:1.0E-6,Neurospora_tetrasperma_tyr2:0.016118); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61705] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_7 = [&R] ((((((((((((((Brugia_malayi_TYR2:0.342198,((((Caenorhabditis_elegans_TYR1:2.0E-6,(Caenorhabditis_briggsae_TYR1:0.0,Caenorhabditis_briggsae_TYR5:0.0):0.016578):0.033007,Caenorhabditis_remanei_TYR1:0.015671):0.094985,Brugia_malayi_TYR3:0.230223):0.076493,((Caenorhabditis_elegans_TYR2:1.0E-6,(Caenorhabditis_remanei_TYR2:0.006296,Caenorhabditis_briggsae_TYR2:0.029757):0.046891):0.131702,Brugia_malayi_TYR4:0.208732):0.058758):0.074767):0.050785,(Brugia_malayi_TYR1:0.192096,(((Caenorhabditis_briggsae_TYR4:0.03047,Caenorhabditis_elgans_TYR4:0.039522):0.030673,Caenorhabditis_remanei_TYR4:1.0E-6):0.060739,((Caenorhabditis_briggsae_TYR3:0.0,Caenorhabditis_remanei_TYR3:0.031578):0.007762,Caenorhabditis_elegans_TYR3:0.015354):0.166143):0.083659):2.0E-6):0.041216,(Caenorhabditis_elegans_TYR5:0.063607,Caenorhabditis_briggsae_TYR6:5.0E-6):0.996858):0.207754,((Caenorhabditis_remanei_TYR5:0.791574,Candidatus_nitrosopumilus_tyr:0.541705):0.14524,((Bacillus_megaterium_tyr1:5.0E-6,Bacillus_megaterium_tyr2:0.008441):0.26215,(Nitrosomonas_europeae_tyr:0.287397,Polysphondylium_pallidum_tyr1:0.415996):0.29348):0.13896):0.188479):0.047553,(Streptomyces_venezuelae_tyr:0.090268,Streptomyces_tsukubaensis_tyr:0.3758):0.365764):0.128286,((((Ectocarpus_siliculosus_tyr4:0.308979,(Ectocarpus_siliculosus_tyr1:0.222857,(Ectocarpus_siliculosus_tyr2:0.063487,Ectocarpus_siliculosus_tyr3:0.027075):0.211173):0.036751):0.041604,(Ectocarpus_siliculosus_tyr5:0.227811,Ectocarpus_siliculosus_tyr6:0.180917):0.275202):0.306885,(((Ectocarpus_siliculosus_tyr12:0.216835,Ectocarpus_siliculosus_tyr13:2.0E-6):0.305503,(((Ectocarpus_siliculosus_tyr16:0.077306,(Ectocarpus_siliculosus_tyr17:0.118915,Ectocarpus_siliculosus_tyr18:0.096113):0.074492):0.018406,Ectocarpus_siliculosus_tyr15:0.268846):0.184646,Ectocarpus_siliculosus_tyr14:0.089658):0.435659):0.379243,((((Ectocarpus_siliculosus_tyr9:0.061214,Ectocarpus_siliculosus_tyr10:0.120544):0.032091,Ectocarpus_siliculosus_tyr11:0.0):0.070223,Ectocarpus_siliculosus_tyr8:0.129314):0.07995,Ectocarpus_siliculosus_tyr7:0.383635):0.180146):0.228555):0.863072,((Dictyostelium_discoideum_tyr1:0.0,Dictyostelium_discoideum_tyr2:0.0):0.688759,((Pinctada_fucata_tyr4:0.239492,(Pinctada_fucata_tyr3:0.008277,Pinctada_fucata_tyr2:0.0):0.156906):0.381108,Phragmatopoma_californica_tyr:0.659943):0.131092):0.082533):0.126856):0.019787,((Nematostella_vectensis_tyr4:0.38019,((Nematostella_vectensis_tyr3:0.133974,Hydra_magnipapillata_tyr:0.910338):0.290044,(Nematostella_vectensis_tyr1:0.886608,Nematostella_vectensis_tyr2:0.89817):0.204411):0.058097):0.481921,(((Glycine_max_CO5:0.29097,((((Glycine_max_CO8:0.156629,(Glycine_max_CO11:0.005064,Glycine_max_CO12:0.043534):0.046689):0.034675,Glycine_max_CO9:0.08463):0.024969,(Oryza_sativa_CO:0.111185,Glycine_max_CO10:0.125284):0.088477):0.055996,((Glycine_max_CO3:0.021233,Glycine_max_CO4:0.039864):0.195703,Vitis_vinifera_CO:0.227543):0.017692):0.042617):0.059421,(Glycine_max_CO2:0.015848,Glycine_max_CO1:0.0):0.185984):0.060193,(Glycine_max_CO6:0.008182,Glycine_max_CO7:1.0E-6):0.180573):1.107658):0.33641):0.115525,(Lottia_gigantea_tyr2:0.950683,((((Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.159414,Sepia_officinalis_tyr:2.0E-6):0.44802,Lottia_gigantea_tyr1:0.24553):0.250728,Pinctada_fucata_tyr1:0.543009):0.117916):0.067031):0.964999,((Lottia_gigantea_Hc:0.960056,(((Ciona_intestinalis_HcB:5.0E-6,((Ciona_intestinalis_HcH:0.018634,Ciona_intestinalis_HcI:0.141023):0.039634,((Ciona_intestinalis_HcE:5.0E-6,Ciona_intestinalis_HcF:0.075234):0.03579,Ciona_intestinalis_HcG:0.199433):0.069364):0.226973):0.092923,(Ciona_intestinalis_HcC:0.085711,Ciona_intestinalis_HcD:2.0E-6):0.22119):2.4E-5,Ciona_intestinalis_HcA:0.062589):0.403789):0.211363,(Sepia_officinalis_Hc:0.293561,(Nucula_nucleus_Hc:0.181866,(Aplysia_californica_Hc:0.123382,Megathura_crenulata_Hc:0.382674):0.127648):0.020438):0.51868):0.366141):0.355787,Agaricus_bisporus_tyr:0.468582):0.177931,Aspergillus_aculeatus_tyr:0.57804):0.169662,(Neurospora_tetrasperma_tyr3:0.0,Neurospora_crassa_tyr3:0.0):0.611834):0.122245,(Neurospora_crassa_tyr2:0.0,Neurospora_tetrasperma_tyr2:0.0):0.350184):0.845283,Neurospora_tetrasperma_tyr1:0.017443,Neurospora_crassa_tyr1:1.0E-6); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61703] END; BEGIN TREES; TITLE Type_3_copper_alpha_subclasss_Maximum_Likelihood; LINK TAXA = TaxaForAnalysisStep11028; TREE bootstrap_20 = [&R] (((((((((((((((((((Caenorhabditis_briggsae_TYR6:2.0E-6,Caenorhabditis_elegans_TYR5:0.036984):0.638398,Brugia_malayi_TYR3:0.24992):0.098873,Brugia_malayi_TYR1:0.089686):0.050452,((Brugia_malayi_TYR4:0.194718,((Caenorhabditis_remanei_TYR2:1.0E-6,(Caenorhabditis_elegans_TYR2:1.0E-6,Caenorhabditis_briggsae_TYR2:0.008834):0.008627):0.042069,(Caenorhabditis_briggsae_TYR5:0.0,(Caenorhabditis_briggsae_TYR1:0.0,(Caenorhabditis_elegans_TYR1:0.0,Caenorhabditis_remanei_TYR1:0.0):0.0):0.0):0.236259):0.038213):0.029282,Brugia_malayi_TYR2:0.351461):0.132209):0.056235,((Caenorhabditis_elgans_TYR4:0.008656,Caenorhabditis_remanei_TYR4:0.016702):0.06889,Caenorhabditis_briggsae_TYR4:1.0E-6):0.060847):0.027705,(Caenorhabditis_elegans_TYR3:1.0E-6,(Caenorhabditis_remanei_TYR3:0.035642,Caenorhabditis_briggsae_TYR3:1.0E-6):0.026088):0.082635):0.141704,Polysphondylium_pallidum_tyr1:0.547757):0.230302,(((Sepia_officinalis_tyr:7.0E-6,(Illex_argentinus_tyr2:0.0,Illex_argentinus_tyr1:0.0):0.04643):0.52022,Nematostella_vectensis_tyr1:0.785553):0.123147,(((Hydra_magnipapillata_tyr:0.955738,Nematostella_vectensis_tyr3:0.144396):0.244037,Nematostella_vectensis_tyr4:0.535044):0.094385,Nematostella_vectensis_tyr2:1.066305):0.371885):0.117861):0.096418,(Pinctada_fucata_tyr1:0.521969,Lottia_gigantea_tyr2:0.668532):0.165421):0.162512,(((((Ectocarpus_siliculosus_tyr8:0.083535,(((Ectocarpus_siliculosus_tyr10:0.172082,Ectocarpus_siliculosus_tyr11:0.028527):0.043674,Ectocarpus_siliculosus_tyr9:0.024111):0.063993,Ectocarpus_siliculosus_tyr7:0.54987):0.067975):0.564793,(Ectocarpus_siliculosus_tyr12:0.162884,Ectocarpus_siliculosus_tyr13:1.0E-6):0.226179):0.332216,((((Ectocarpus_siliculosus_tyr18:0.105747,Ectocarpus_siliculosus_tyr17:0.049269):0.078884,Ectocarpus_siliculosus_tyr16:0.098283):0.123918,Ectocarpus_siliculosus_tyr15:0.12362):0.254067,Ectocarpus_siliculosus_tyr14:0.017828):0.27815):0.457974,((Ectocarpus_siliculosus_tyr5:0.34611,Ectocarpus_siliculosus_tyr6:0.293049):0.317993,((Ectocarpus_siliculosus_tyr1:0.137882,(Ectocarpus_siliculosus_tyr2:0.056279,Ectocarpus_siliculosus_tyr3:0.056476):0.194888):0.030789,Ectocarpus_siliculosus_tyr4:0.224844):0.072779):0.445172):0.565036,((Dictyostelium_discoideum_tyr1:0.008262,Dictyostelium_discoideum_tyr2:0.018794):0.697735,(Phragmatopoma_californica_tyr:0.362423,((Pinctada_fucata_tyr2:0.0,Pinctada_fucata_tyr3:0.0):0.163564,Pinctada_fucata_tyr4:0.206207):0.272041):0.134976):0.030145):0.181844):0.031241,(Lottia_gigantea_tyr1:0.233571,Caenorhabditis_remanei_TYR5:0.790881):0.161783):0.243866,(((Bacillus_megaterium_tyr2:0.009123,Bacillus_megaterium_tyr1:1.0E-6):0.094358,(Nitrosomonas_europeae_tyr:0.484017,(Streptomyces_venezuelae_tyr:0.237586,Streptomyces_tsukubaensis_tyr:0.170526):0.132392):0.165791):0.257855,Candidatus_nitrosopumilus_tyr:0.414732):1.1E-5):0.066284,((Glycine_max_CO12:0.037981,((((Glycine_max_CO6:0.0,Glycine_max_CO7:0.019878):0.233674,(Vitis_vinifera_CO:0.16477,(Glycine_max_CO4:0.004463,Glycine_max_CO3:0.023935):0.263879):0.072103):3.0E-6,((Glycine_max_CO2:0.0,Glycine_max_CO1:0.0):0.069856,Glycine_max_CO5:0.263473):0.076807):0.087944,((Oryza_sativa_CO:0.262779,Glycine_max_CO8:0.123172):0.063513,Glycine_max_CO9:0.077843):0.039678):0.097242):0.027608,(Glycine_max_CO10:0.106493,Glycine_max_CO11:1.0E-6):2.0E-6):1.596117):0.488569,((((Megathura_crenulata_Hc:0.236653,Aplysia_californica_Hc:0.220767):0.074781,Nucula_nucleus_Hc:0.219791):0.133794,Sepia_officinalis_Hc:0.202738):0.378925,((Ciona_intestinalis_HcB:4.0E-6,Ciona_intestinalis_HcC:0.073639):0.076596,(((((Ciona_intestinalis_HcF:0.111733,Ciona_intestinalis_HcE:2.0E-6):0.02934,(Ciona_intestinalis_HcI:0.085933,Ciona_intestinalis_HcH:0.014904):0.14144):0.009923,Ciona_intestinalis_HcG:0.252263):0.32379,Ciona_intestinalis_HcA:5.0E-6):0.38335,Ciona_intestinalis_HcD:0.028049):0.062501):0.761395):0.331271):0.114921,Lottia_gigantea_Hc:0.765394):0.416726,((Neurospora_tetrasperma_tyr1:0.018904,Neurospora_crassa_tyr1:1.0E-6):0.662268,Agaricus_bisporus_tyr:0.370576):0.243186):0.105912,Aspergillus_aculeatus_tyr:0.570426):0.158567,(Neurospora_crassa_tyr3:0.0,Neurospora_tetrasperma_tyr3:0.0):0.414776):0.467072,Neurospora_crassa_tyr2:1.0E-6,Neurospora_tetrasperma_tyr2:0.008913); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61716] END;