#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 19, 2025; 10:56 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 11035 ] BEGIN TAXA; TITLE TaxaForAnalysisStep11035; DIMENSIONS NTAX=46; TAXLABELS 'Branchiostoma floridae tyr1/2a' 'Branchiostoma floridae tyr1/2b' Branchiostoma_floridae_tyrA1 Branchiostoma_floridae_tyrB1 Branchiostoma_floridae_tyrC1 Branchiostoma_floridae_tyra Branchiostoma_floridae_tyrb Branchiostoma_floridae_tyrc Branchiostoma_floridae_tyrd Branchiostoma_floridae_tyre Branchiostoma_floridae_tyrf Branchiostoma_floridae_tyrg Branchiostoma_floridae_tyrh Branchiostoma_floridae_tyri Branchiostoma_floridae_tyrj Branchiostoma_floridae_tyrk Branchiostoma_floridae_tyrl Branchiostoma_floridae_tyrm Capitella_teleta_tyr1 Capitella_teleta_tyr2 Ciona_intestinalis_tyr 'Ciona intestinalis tyr1/2a' 'Ciona intestinalis tyr1/2b' Clonorchis_sinensis_tyr2 Clonorchis_sinensis_tyr3 Clonorchis_sinensis_tyr4 Clonorchis_sinensis_tyr5 Clonorhis_sinensis_tyr1 Homo_sapiens_TYR Homo_sapiens_TYRP1 Homo_sapiens_TYRP2a Homo_sapiens_TYRP2b Mus_musculus_Tyr Mus_musculus_Tyrp1 Mus_musculus_Tyrp2 Saccoglossus_kowalevskii_tyra Saccoglossus_kowalevskii_tyrb Saccoglossus_kowalevskii_tyrc Saccoglossus_kowalevskii_tyrd Schistosoma_japonicum_tyr Schistosoma_mansoni_try2 Schistosoma_mansoni_tyr1 Schistosoma_mansoni_tyr3 Schistosoma_mansoni_tyr4 Schmidtea_mediterranea_tyr Suberites_domuncula_tyr ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M16283] TITLE alignment_gammatype; LINK TAXA = TaxaForAnalysisStep11035; DIMENSIONS NCHAR=149; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 ] [ . . . . . . . . . . . . . . ] 'Branchiostoma floridae tyr1/2a' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREIQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRGRDVGRCLSFRNTLEGFSLHNLAHLFLNGTASITHASANDPIFVLLHSYSDAIFW 'Branchiostoma floridae tyr1/2b' HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW Branchiostoma_floridae_tyrA1 HYYVVRNVLLHEGPAFLPWHRLYLLLLERELAKIIGDENFALPYWDWRDLADTNDFFGASLDSSGSFLSGWQIVCCDGTPEGPLQRNPGKSLPTWEEVQGALSFRNSLEGFYLHAAVHVWMNGTVSLPAASPNDPVFFLHHAFVDSIYW Branchiostoma_floridae_tyrB1 HYYVSMDALLHEAPAFLPWHRLFLLRWEQEIQKLTGDENFTIPYWDWRDAEKTDEYMGGQHTSPASFFSSWQIVCCNGTPEGPLRRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFW Branchiostoma_floridae_tyrC1 HYYVSRDTLLHEAPGFLPWHRLFLLLWEQEIRELTGDENFTVPYWDWRDAENTDEYLGGRHESPASFFSSWQIICCDGTPEGPLLRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIFMNGTMSQVQGSANDPIFLLHHAFVDSIFW Branchiostoma_floridae_tyra HYYASRDTMPHEGVGFPTWHRAYVLEIERALQEVNNDPDWTLPYWDWSAAAKTNEYVGSNDNDSESAFTSWGTICCDVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGFTVHNQVHIYLNGTMSSVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrb HYYASRATMPHKGPAFTTWHRAYLLEFERAVQVVNNDPDWTLPYWDWSAAEDTNEYVGANDDDSGSVFASWGIICCDVTVLGKLNRNPGQHLPLVTEVDFALSFRNLLEGYSMHNQVHIYLNGTMSHVPSAPNDPMFFLHHCNVDRLFW Branchiostoma_floridae_tyrc HYYASRDTMPHEGVGFPTWHRAYLLEFERAVQEVNDDPDWTVPYWDWSAAEDTNEYVGKNDDEPESVFASWWTICCNVTVTGTLKRNPGKHLPLATEVDFALTFRNLLEGYTLHNHVHLYLDGTMSNVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyrd HYYASRATTPHEGAGFPTWHRAYLLEFDRAVQEVNNDPDWTLPYWDWGAAEDTNEYVGANDDDSRSVFASWGTICCNVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGTTMHNQVHIYLNGTMSHVPSAANDPTFFLHHCNVDRLLW Branchiostoma_floridae_tyre HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGKNSSNILGEFSGWKDLCCSNNNLPSITRNPGGELPSLEALYYTLSFRNILEGFQSHNQVHSYMNGTMGVVETSPNDPMFWLHHSNVDRIMW Branchiostoma_floridae_tyrf HYYSVWDNIVHSGPGFPTWHRSFIQLWEMALQKVSNNEEFALPYWDWAGEPNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGYQLHNQVHLYFNGTISVIANAPSDPIFILHHVNVDRILW Branchiostoma_floridae_tyrg HYYVSRDNIRHGGPGFPTWHRYFMLLWERALQKVSNNEEFALPYWDWAGELNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGFQLHNQVHIYLNGTMSDVPIAPNDPIFILHHSNVDRIFW Branchiostoma_floridae_tyrh HNFIARDGTQHSGPSFPVWHRRYMLTVEKEFQRIMGNDTFGFPYWQWEENDMTPEYFGVPASVSGSLVQDWNTICCNPALARPVQRGGGSYLPNTVEVMISLSFRSRLEGWHMHNNVHVWVGGQMDVVPAAVNDPIFNLHHCNVDRIFW Branchiostoma_floridae_tyri HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGENSSNILGEFSGWKDLCCSNVNLPSITRHPGSELPSLDALYYTLSFRNILEGFQSQNRVHSYLNGTMGIVASSPNDPMFWLHHSNVDRIMW Branchiostoma_floridae_tyrj HYYASRETLPHEGAGFPTWHRAFLLEAERALQEVNGDPDWTLPYWDWSAAEQTNEYVGTNDHDSESIFATWRTICCDVTPTGRLKRNPGHRLPLATEVDFALSFRNLLDGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHSNVDRLFW Branchiostoma_floridae_tyrk HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyrl HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW Branchiostoma_floridae_tyrm HYYASRETLPHEGAGFPTWHRAFLQEAERALQEVNGDPDWTIPYWDWSAAEQTNEYVGANDGDSESSFATWRTLCCDVTPTGRLKRNPGHRLPLATEVDFALNFRNLLEGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHANVDRLFW Capitella_teleta_tyr1 HYFSTKNAEVHNGPGFLTWHRLYLMMMEREMGRVAGDPFFALPYWNWSGAGVTDDLAGSINSSTGSPFSRWESACCDLRPRGPVIRDPEAFLPPMEDVIFTLSFRNCIEGFTMHIQVHSFFRGTISQVSSSPDDPLFFFHHTYIDKLFW Capitella_teleta_tyr2 HFFSVKTPIKHNGPGFPTWHRRFLLEFERELQRASGDEQMGIPYWDWTDHAHTNDLVGEMVDDRGSDFWNWTMRCCNMSPPSQIWRLPTGNLPILEDISFALSFRNCLEGFSLHGQGHTFFSGSVNAVPISPSDPLFYLHHAYVDKILW Ciona_intestinalis_tyr HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTTLPTWQDVLDVLSFVNSLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW 'Ciona intestinalis tyr1/2a' HAYVSRDNLVHEGPAFLPWHRYYLLKWEQELRDVVNDVTFTIPYWDWRDNQDNDVMMGGNDDSQGSPISKWEIICCTGASEGPLLRSPGNGLPTSQEVDDVISFRNLVEGFYLHNAVHLFMNGTMSEVATSANDPIFVLHHAYVDSLYW 'Ciona intestinalis tyr1/2b' HYYAVRDTLLHEGPAYNTWHRMHLLWLEREIQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRGRDVGRCLSFRNTLEGFSLHNLAHLFLNGTASITHASANDPIFVLLHSYSDAIFW Clonorchis_sinensis_tyr2 HRYGSRSTLYHDGVCFPTWHRYYILLWERLMSRITGITDYATPYWDWVGLKHTNRYIGAPGESTGSPFHNLTEYCCQRGNRGTITRNFYRDLPDIDDLKFVLSFHMALEGFWFHNKVHVLIDGSMCCTGTASNDPIFVLHHALTDKIFW Clonorchis_sinensis_tyr3 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFV Clonorchis_sinensis_tyr4 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Clonorchis_sinensis_tyr5 HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW Clonorhis_sinensis_tyr1 HNYSSRTTLYHDGPEFPTWHRYLMLIWERLLAEIAGIKDFTLPYWDWVGLLKDNKYVGAPGKDSESIFYNVTNYCCQAGRAGKLVRRFVSVFPTQADVAFVLSFHMALEGFWMHNKVHNMIDGAMRSTATATNDPFFILHHNFVDKLLW Homo_sapiens_TYR HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP1 HYYAVRDTLLHEGPAYNTWHRMHLLWLEREMQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRPEDVGRCLSFRNSLEGYSLHNLAHLFLNGTGGITHASANDPIFVLLHSYSDAIFW Homo_sapiens_TYRP2a HYYSVKKTFLHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEDGPIRRNPAGRLPEPQDVAQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Homo_sapiens_TYRP2b HYYSVRDTLLHQGPAFVTWHRYHLLWLERELQRLTGNESFALPYWNFATGKNTDELLGAARDSRNSRFSTWEIVCCNGTYEGLLRRNKVGKLPTLKNVQDCLSFRNALEGFNLHNLAHSFLNGTNALPHSAANDPVFVVLHSFTDAIFW Mus_musculus_Tyr HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTSLPTWQDVRDVLSFVNTLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW Mus_musculus_Tyrp1 HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW Mus_musculus_Tyrp2 HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW Saccoglossus_kowalevskii_tyra HYYASRETILHDAVGFLTWHRGYLLEMERLIQEVNNDPDWALPYWDWTVSEQTNDFVGANDNDSGSAFAGWEVLCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Saccoglossus_kowalevskii_tyrb HYYASRETILHDAVGFLTWHRGYLLEMERSIQEVNNDPDWAIPYWDWTVSEQTNDFVGANDNDSGSAFAGWEALCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW Saccoglossus_kowalevskii_tyrc HYYASRATMPHEGSGFPTWHRAFLLDLERALQEVNNDPDFTIPYWDWTEAENTNDYVGANYDDPRSLFATWETICCNVTRDGHVMRNPGHRLPTAAEVDFGLTFRNLLEGFTLHNHVHLYLDGTMSAVPSSANDPIFFLHHCFVDRIFW Saccoglossus_kowalevskii_tyrd HYYASRATMPHEGVGFPTWHRAYVLEFERAVQEVNDDSDWTLPYWDWSAAEDTNDYVGKNDDDTGSVFANWETICCNVTGTGKLKRNPGNRLPYTTEVDFALSFRNLLEGYTLHNHVHIYLDGTMSDVPSAANDPIFFLHHCNVDRLFW Schistosoma_japonicum_tyr HRYASRATLFHEVVGFLTWHRYYMLFWERHLRKIAGWTDFTIPYWDWVDSTRVNSLLGGYGGDPRSPFYMWPEYCCHAGNFRVLTRYFESAFPTTHNLLFTLGFHQALEGFFMHNKVHNVVSGTFCCAATSPNDPLFLVHHTQIDRIFW Schistosoma_mansoni_try2 HEYASRGTLYHHVLGFATWHRYFMLVWERQLRKIAGWKDFAVPYWDWIDADKVNSLVGAPGDHRDSPFSNWTEQCCHSANFKPLNRHYKQAFPTTKDLQFTLGFHQALEGFFMHNKVHNMVHGSFCCASTAANDPLFLLHHSQIDRIMW Schistosoma_mansoni_tyr1 HRYGARPTLYHDGVTFPTWHRYFQLIWERMLSNIAGIHNFAVPYWDMIGLEKTDDYVGGPGRSPNSAFTGFQEYCCQGTPNTTITRQFLTAFPNQEDLYFTLSFHMALEGYWMHNRLHRMINGSMCCTSTATNDPIFIVLHNFVDKIFW Schistosoma_mansoni_tyr3 HFYASRSTMSHKGPAFFTWHRHYLLMFEDLLRSIAGYFNFTLPYWDWTNQTTTNDLLGDIPEESNSTFFKWKPICCDPSEEPFLWRKYSSRLPNQNEIDELFSFRNFAEGYMMHNMVHSFINGTWMDFTTSPNDPLFLLHHTFMDKIFW Schistosoma_mansoni_tyr4 HVYASRSTLTHKGPGFPTWHRAYVLFVEEELGRLTDGDNFALPYWDWTGQTGTTDLVGAFLNLDSSPFADWVTFCCDPGLTSNGRKSPMARLPDQLDVDITLSFRDLLEGFHMHNLVHSYFNGSWFDVATSPNDPIFFLHHTFVDKLFW Schmidtea_mediterranea_tyr NSYGSRTTLYHDGPTFPTWHRYLMLIWERMLAEIAGIKNFALPYWDWVGLLKDNKYVGAPGRDSRSIFYNATNYCCQAGRVGKLVRKFVSVFPNQADIAFILSFHMALEGFWTNNKVHNMIEGSMQRTATATNDPIYILHQVFIDKLLW Suberites_domuncula_tyr QYYAGVHSFPQGSAGFATWNRAFLVAFELAVQVVNADYDFALPYYDWTESSSSNDLVGANNSDDMSVFSRWNTVCCDVNDTGPIIRKADGSLPAKKEVNFAQSFRNLLEGFYLNEQVHQSLGGTMSQLWQASNDPIFYLHRCFMDRIFW ; END; [ The following blocks are output data for analysis step 11035 ] BEGIN TREES; TITLE Type_3_copper_gamma_subclass_Neighbor_Joining; LINK TAXA = TaxaForAnalysisStep11035; TREE tree_1 = [&R] (Suberites_domuncula_tyr:0.4093585,((((Saccoglossus_kowalevskii_tyrd:0.015356,Saccoglossus_kowalevskii_tyrc:0.150204):0.210048,(Saccoglossus_kowalevskii_tyrb:0.024127,Saccoglossus_kowalevskii_tyra:0.054663):0.303809):0.147026,(Branchiostoma_floridae_tyrm:0.654695,((Branchiostoma_floridae_tyrk:0.011014,Branchiostoma_floridae_tyrj:0.010017):0.240518,(Branchiostoma_floridae_tyrl:0.132607,((Branchiostoma_floridae_tyra:0.025046,Branchiostoma_floridae_tyrb:0.040085):0.090832,((Branchiostoma_floridae_tyrd:1.0E-6,Branchiostoma_floridae_tyrc:1.0E-6):0.138269,((Branchiostoma_floridae_tyre:0.1057,Branchiostoma_floridae_tyri:0.054588):0.027601,(Branchiostoma_floridae_tyrf:0.084565,(Branchiostoma_floridae_tyrh:0.084864,Branchiostoma_floridae_tyrg:0.06425):0.026695):0.008586):0.015913):0.041157):0.075061):0.025366):0.045025):0.122036):0.037612,(((Capitella_teleta_tyr2:0.55833,Capitella_teleta_tyr1:0.492036):0.104517,((Clonorhis_sinensis_tyr1:0.433646,Schmidtea_mediterranea_tyr:0.489522):0.106003,((Schistosoma_mansoni_tyr1:0.264712,Clonorchis_sinensis_tyr2:0.210759):0.221774,((Clonorchis_sinensis_tyr3:0.326621,(Clonorchis_sinensis_tyr5:0.036723,Clonorchis_sinensis_tyr4:0.166253):0.27665):0.017449,(Schistosoma_japonicum_tyr:0.106704,(Schistosoma_mansoni_try2:0.0,(Schistosoma_mansoni_tyr4:0.0,Schistosoma_mansoni_tyr3:0.01773):0.005458):0.160301):0.211953):0.095254):0.343117):0.092196):0.004438,(((Mus_musculus_Tyr:0.043994,Homo_sapiens_TYR:0.068203):0.175262,(Ciona_intestinalis_tyr:0.345373,(Branchiostoma_floridae_tyrA1:0.201658,(Branchiostoma_floridae_tyrC1:0.013587,Branchiostoma_floridae_tyrB1:0.007658):0.231828):0.075852):0.030293):0.073208,((Mus_musculus_Tyrp2:0.063577,(Homo_sapiens_TYRP2a:1.0E-6,Homo_sapiens_TYRP2b:1.0E-6):0.052295):0.215784,(('Branchiostoma floridae tyr1/2b':0.029886,'Branchiostoma floridae tyr1/2a':0.021976):0.194567,((Mus_musculus_Tyrp1:0.006799,Homo_sapiens_TYRP1:0.021357):0.258472,('Ciona intestinalis tyr1/2b':0.051062,'Ciona intestinalis tyr1/2a':0.08612):0.106496):0.036934):0.038062):0.252273):0.12314):0.022078):0.4093585); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr61790] END;