#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 18, 2025; 23:02 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]

BEGIN TAXA;
        TITLE  Taxa;
        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_tyr1
            Schistosoma_mansoni_tyr2
            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:M16282]

	TITLE gamma_alignment_ML;
	LINK TAXA = Taxa;
	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'   HYYAVRDTLLHEGPAYNTWHRMHLLWLEREMQKMLGDETFALHYWDWAVGGTTDDMMGARHLSPGSPFSRWQSVCCNGTDEGPIFRNPGGVLPRPEDVGRCLSFRNSLEGYSLHNLAHLFLNGTGGITHASANDPIFVLLHSYSDAIFW
Branchiostoma_floridae_tyrA1       HYYVVRNVLLHEGPAFLPWHRLYLLLLERELAKIIGDENFALPYWDWRDLADTNDFFGASLDSSGSFLSGWQIVCCDGTPEGPLQRNPGKSLPTWEEVQGALSFRNSLEGFYLHAAVHVWMNGTVSLPAASPNDPVFFLHHAFVDSIYW
Branchiostoma_floridae_tyrB1       HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTSLPTWQDVRDVLSFVNTLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW
Branchiostoma_floridae_tyrC1       HYYVSRNVLLHEGPVFLPWHRLFLLLWERELARFVDDENFAIPYWDWRGLDGTDDFLGATPNSNETVFSDWQVICCDGSPEGPLLRNPGTTLPTWQDVLDVLSFVNSLEGFYLHNAVHRFMNGTLSSVGSSANDPIFIIHHAYVDSIYW
Branchiostoma_floridae_tyra        HYYASRETLPHEGAGFPTWHRAFLLEAERALQEVNGDPDWTLPYWDWSAAEQTNEYVGTNDHDSESIFATWRTICCDVTPTGRLKRNPGHRLPLATEVDFALSFRNLLDGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHSNVDRLFW
Branchiostoma_floridae_tyrb        HYYASRETLPHEGAGFPTWHRAFLQEAERALQEVNGDPDWTIPYWDWSAAEQTNEYVGANDGDSESSFATWRTLCCDVTPTGRLKRNPGHRLPLATEVDFALNFRNLLEGFTLHNHVHLYLNGTMSTVITAANDPIFLLHHANVDRLFW
Branchiostoma_floridae_tyrc        HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW
Branchiostoma_floridae_tyrd        HYYASRETMPHDGSGFLTWHRAYVLEVERALQEVNGDPDWTMPYWDWGAAEKTNEYVGANNHDTGSLFASWRTICCNVTASGKLKRNPGHHLPLATEVDFALSFRNLLEGNTLHDEVHIYLNGTMSNVPTAPNDPMFFLHHCNVDRLLW
Branchiostoma_floridae_tyre        HYYASRDTMPHEGVGFPTWHRAYLLEFERAVQEVNDDPDWTVPYWDWSAAEDTNEYVGKNDDEPESVFASWWTICCNVTVTGTLKRNPGKHLPLATEVDFALTFRNLLEGYTLHNHVHLYLDGTMSNVPSAANDPTFFLHHCNVDRLLW
Branchiostoma_floridae_tyrf        HYYASRDTMPHEGVGFPTWHRAYVLEIERALQEVNNDPDWTLPYWDWSAAAKTNEYVGSNDNDSESAFTSWGTICCDVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGFTVHNQVHIYLNGTMSSVPSAANDPTFFLHHCNVDRLLW
Branchiostoma_floridae_tyrg        HYYASRATMPHKGPAFTTWHRAYLLEFERAVQVVNNDPDWTLPYWDWSAAEDTNEYVGANDDDSGSVFASWGIICCDVTVLGKLNRNPGQHLPLVTEVDFALSFRNLLEGYSMHNQVHIYLNGTMSHVPSAPNDPMFFLHHCNVDRLFW
Branchiostoma_floridae_tyrh        HYYASRATTPHEGAGFPTWHRAYLLEFDRAVQEVNNDPDWTLPYWDWGAAEDTNEYVGANDDDSRSVFASWGTICCNVTVLGKLKRNPGKRLPLATEVDFALSFRNLLEGTTMHNQVHIYLNGTMSHVPSAANDPTFFLHHCNVDRLLW
Branchiostoma_floridae_tyri        HYYASRATMPHEGVGFPTWHRAYVLEFERAVQEVNDDSDWTLPYWDWSAAEDTNDYVGKNDDDTGSVFANWETICCNVTGTGKLKRNPGNRLPYTTEVDFALSFRNLLEGYTLHNHVHIYLDGTMSDVPSAANDPIFFLHHCNVDRLFW
Branchiostoma_floridae_tyrj        HYYASRETILHDAVGFLTWHRGYLLEMERLIQEVNNDPDWALPYWDWTVSEQTNDFVGANDNDSGSAFAGWEVLCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW
Branchiostoma_floridae_tyrk        HYYASRETILHDAVGFLTWHRGYLLEMERSIQEVNNDPDWAIPYWDWTVSEQTNDFVGANDNDSGSAFAGWEALCCDPNPPEKLKRNPGTELPRKEEVDFALVFRNLVEGYTLHNHVHLYLNGTMSDVPSSANDPIFWLHHAFIDRIFW
Branchiostoma_floridae_tyrl        HYYASRATMPHEGSGFPTWHRAFLLDLERALQEVNNDPDFTIPYWDWTEAENTNDYVGANYDDPRSLFATWETICCNVTRDGHVMRNPGHRLPTAAEVDFGLTFRNLLEGFTLHNHVHLYLDGTMSAVPSSANDPIFFLHHCFVDRIFW
Branchiostoma_floridae_tyrm        QYYAGVHSFPQGSAGFATWNRAFLVAFELAVQVVNADYDFALPYYDWTESSSSNDLVGANNSDDMSVFSRWNTVCCDVNDTGPIIRKADGSLPAKKEVNFAQSFRNLLEGFYLNEQVHQSLGGTMSQLWQASNDPIFYLHRCFMDRIFW
Capitella_teleta_tyr1              HYFSTKNAEVHNGPGFLTWHRLYLMMMEREMGRVAGDPFFALPYWNWSGAGVTDDLAGSINSSTGSPFSRWESACCDLRPRGPVIRDPEAFLPPMEDVIFTLSFRNCIEGFTMHIQVHSFFRGTISQVSSSPDDPLFFFHHTYIDKLFW
Capitella_teleta_tyr2              HFFSVKTPIKHNGPGFPTWHRRFLLEFERELQRASGDEQMGIPYWDWTDHAHTNDLVGEMVDDRGSDFWNWTMRCCNMSPPSQIWRLPTGNLPILEDISFALSFRNCLEGFSLHGQGHTFFSGSVNAVPISPSDPLFYLHHAYVDKILW
Ciona_intestinalis_tyr             HAYVSRDNLVHEGPAFLPWHRYYLLKWEQELRDVVNDVTFTIPYWDWRDNQDNDVMMGGNDDSQGSPISKWEIICCTGASEGPLLRSPGNGLPTSQEVDDVISFRNLVEGFYLHNAVHLFMNGTMSEVATSANDPIFVLHHAYVDSLYW
'Ciona intestinalis tyr1/2a'       HYYSVRDTLLHEGPAFLTWHRMHLMGLENDLQVLSNDPTFALPYWDFAIGGSTDDILGGQNNGPNSTFADWEVVCCNGTFEGPIRRNPGGTLPATEDVIKCLSFRNALEGYTLHNLAHLFLNGTGGMTHASANDPVFVLLHTFTDAIFW
'Ciona intestinalis tyr1/2b'       HYYSVRDTLLHEGPAFLTWHRMHLLGLENDLQDLSGDPTFALPYWDFAIGGTTDELLGGQETGSNSRFADWEVVCCNGTNEGPIRRNPGGSLPVPEDVAECLSFRNALEGYTLHNLAHLFLNGTGGMTHASANDPIFVLLHTFTDAIFW
Clonorchis_sinensis_tyr2           HEYASRGTLYHHVLGFATWHRYFMLVWERQLRKIAGWKDFAVPYWDWIDADKVNSLVGAPGDHRDSPFSNWTEQCCHSANFKPLNRHYKQAFPTTKDLQFTLGFHQALEGFFMHNKVHNMVHGSFCCASTAANDPLFLLHHSQIDRIMW
Clonorchis_sinensis_tyr3           HRYGARPTLYHDGVTFPTWHRYFQLIWERMLSNIAGIHNFAVPYWDMIGLEKTDDYVGGPGRSPNSAFTGFQEYCCQGTPNTTITRQFLTAFPNQEDLYFTLSFHMALEGYWMHNRLHRMINGSMCCTSTATNDPIFIVLHNFVDKIFW
Clonorchis_sinensis_tyr4           NSYGSRTTLYHDGPTFPTWHRYLMLIWERMLAEIAGIKNFALPYWDWVGLLKDNKYVGAPGRDSRSIFYNATNYCCQAGRVGKLVRKFVSVFPNQADIAFILSFHMALEGFWTNNKVHNMIEGSMQRTATATNDPIYILHQVFIDKLLW
Clonorchis_sinensis_tyr5           HNYSSRTTLYHDGPEFPTWHRYLMLIWERLLAEIAGIKDFTLPYWDWVGLLKDNKYVGAPGKDSESIFYNVTNYCCQAGRAGKLVRRFVSVFPTQADVAFVLSFHMALEGFWMHNKVHNMIDGAMRSTATATNDPFFILHHNFVDKLLW
Clonorhis_sinensis_tyr1            HVYASRSTLTHKGPGFPTWHRAYVLFVEEELGRLTDGDNFALPYWDWTGQTGTTDLVGAFLNLDSSPFADWVTFCCDPGLTSNGRKSPMARLPDQLDVDITLSFRDLLEGFHMHNLVHSYFNGSWFDVATSPNDPIFFLHHTFVDKLFW
Homo_sapiens_TYR                   HYYVSMDALLHEAPAFLPWHRLFLLRWEQEIQKLTGDENFTIPYWDWRDAEKTDEYMGGQHTSPASFFSSWQIVCCNGTPEGPLRRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIYMNGTMSQVQGSANDPIFLLHHAFVDSIFW
Homo_sapiens_TYRP1                 HYYSVKKTFLHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEDGPIRRNPAGRLPEPQDVAQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW
Homo_sapiens_TYRP2a                HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW
Homo_sapiens_TYRP2b                HYYSVRDTLLHQGPAFVTWHRYHLLCLERDLQRLIGNESFALPYWNFATGRNTDQLFGAARDSRNSRFSSWETVCCNGTYEGLLRRNQMGKLPTLKDIRDCLSFRNALEGFSLHNLVHSFLNGTNALPHSAANDPIFVVLHSFTDAIFW
Mus_musculus_Tyr                   HYYVSRDTLLHEAPGFLPWHRLFLLLWEQEIRELTGDENFTVPYWDWRDAENTDEYLGGRHESPASFFSSWQIICCDGTPEGPLLRNPGNRLPSSADVEFCLSFRNTLEGFSMHNALHIFMNGTMSQVQGSANDPIFLLHHAFVDSIFW
Mus_musculus_Tyrp1                 HYYSVKKTFLHEGPAFLTWHRYHLLQLERDMQEMLQEPSFSLPYWNFATGKNTDDLMGSRSFSPNSVFSQWRVVCCNSTEGGPIRRNPAGRLPEPQDVTQCLSFRNTVEGYSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFW
Mus_musculus_Tyrp2                 HYYSVRDTLLHQGPAFVTWHRYHLLWLERELQRLTGNESFALPYWNFATGKNTDELLGAARDSRNSRFSTWEIVCCNGTYEGLLRRNKVGKLPTLKNVQDCLSFRNALEGFNLHNLAHSFLNGTNALPHSAANDPVFVVLHSFTDAIFW
Saccoglossus_kowalevskii_tyra      HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGENSSNILGEFSGWKDLCCSNVNLPSITRHPGSELPSLDALYYTLSFRNILEGFQSQNRVHSYLNGTMGIVASSPNDPMFWLHHSNVDRIMW
Saccoglossus_kowalevskii_tyrb      HYYAARENIRHAGPAFLTWHRAYLLLFERMIQQVNNDDDFAIPYWDWSGAPNTEEYMGKNSSNILGEFSGWKDLCCSNNNLPSITRNPGGELPSLEALYYTLSFRNILEGFQSHNQVHSYMNGTMGVVETSPNDPMFWLHHSNVDRIMW
Saccoglossus_kowalevskii_tyrc      HYYSVWDNIVHSGPGFPTWHRSFIQLWEMALQKVSNNEEFALPYWDWAGEPNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGYQLHNQVHLYFNGTISVIANAPSDPIFILHHVNVDRILW
Saccoglossus_kowalevskii_tyrd      HYYVSRDNIRHGGPGFPTWHRYFMLLWERALQKVSNNEEFALPYWDWAGELNTDTYFGKSTDTVTGTFANWPAICCSNTNTPRIQRNPGGVLPSKEAVYYALSFRNVLEGFQLHNQVHIYLNGTMSDVPIAPNDPIFILHHSNVDRIFW
Schistosoma_japonicum_tyr          HRYGSRSTLYHDGVCFPTWHRYYILLWERLMSRITGITDYATPYWDWVGLKHTNRYIGAPGESTGSPFHNLTEYCCQRGNRGTITRNFYRDLPDIDDLKFVLSFHMALEGFWFHNKVHVLIDGSMCCTGTASNDPIFVLHHALTDKIFW
Schistosoma_mansoni_tyr1           HRYASRATLFHEVVGFLTWHRYYMLFWERHLRKIAGWTDFTIPYWDWVDSTRVNSLLGGYGGDPRSPFYMWPEYCCHAGNFRVLTRYFESAFPTTHNLLFTLGFHQALEGFFMHNKVHNVVSGTFCCAATSPNDPLFLVHHTQIDRIFW
Schistosoma_mansoni_tyr2           HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW
Schistosoma_mansoni_tyr3           HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFV
Schistosoma_mansoni_tyr4           HRYGSRSTLYHDGVCFPTWHRYYGLLWERLMSKIAGITDFATPYWDWTGLTYTNRYIGAPGDSSRSPFSNLTEFCCQKSKRLTITREFKKNLPDVEDLKYVLSFNIALEGFWFHNKLHVLVDGSMCCTGTASNDPLFILHHTFIDKIFW
Schmidtea_mediterranea_tyr         HFYASRSTMSHKGPAFFTWHRHYLLMFEDLLRSIAGYFNFTLPYWDWTNQTTTNDLLGDIPEESNSTFFKWKPICCDPSEEPFLWRKYSSRLPNQNEIDELFSFRNFAEGYMMHNMVHSFINGTWMDFTTSPNDPLFLLHHTFMDKIFW
Suberites_domuncula_tyr            HNFIARDGTQHSGPSFPVWHRRYMLTVEKEFQRIMGNDTFGFPYWQWEENDMTPEYFGVPASVSGSLVQDWNTICCNPALARPVQRGGGSYLPNTVEVMISLSFRSRLEGWHMHNNVHVWVGGQMDVVPAAVNDPIFNLHHCNVDRIFW
;
END;