#NEXUS [written Tue Jun 28 11:29:51 BST 2016 by Mesquite version 3.04 (build 725) at DESKTOP-RN1VH2J/10.0.10.15] BEGIN TAXA; TITLE P_gene; DIMENSIONS NTAX=36; TAXLABELS Phocine_distemper_virus_KC802221 Canine_distemper_virus_AY649446 Measles_virus_NC001498 Cetacean_morbillivirus_KF711855 Cetacean_morbillivirus_JX195718 Pilot_whale_morbillivirus_FJ842381 Pilot_whale_morbillivirus_AF200817 Porpoise_morbillivirus_KF650727 Dolphin_morbillivirus_EF451565 Dolphin_morbillivirus_KC888945 Dolphin_morbillivirus_KJ139453 Dolphin_morbillivirus_KJ139452 Dolphin_morbillivirus_JN210891 Dolphin_morbillivirus_KF695110 Dolphin_morbillivirus_KR704575 Dolphin_morbillivirus_KR337460 Dolphin_morbillivirus_HQ829972 Dolphin_morbillivirus_HQ829973 Dolphin_morbillivirus_KP835995 Dolphin_morbillivirus_EU039963 Dolphin_morbillivirus_KJ139451 Dolphin_morbillivirus_AJ608288 Dolphin_morbillivirus_AF333347 Dolphin_morbillivirus_KP835987 Dolphin_morbillivirus_KP835983 Dolphin_morbillivirus_KP835991 Dolphin_morbillivirus_KT878657 Dolphin_morbillivirus_KC572861 Dolphin_morbillivirus_KP835999 Dolphin_morbillivirus_KT878656 Dolphin_morbillivirus_KT878659 Dolphin_morbillivirus_KT878658 Dolphin_morbillivirus_KT878660 Dolphin_morbillivirus_KT878661 Dolphin_morbillivirus_KP836003 Dolphin_morbillivirus_KJ139454 ; END; BEGIN CHARACTERS; TITLE P_gene_alignment; DIMENSIONS NCHAR=309; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Phocine_distemper_virus_KC802221 CAGAACATTGCTATCTCGACAATGGGACACTTATCGAGTATCATGATTGC-----TTTGGAAAGGATACCGGAGATCCCACTGCAAATGTCCTGAGCTTCTTGCTGAGGTCCTAAAGAAGCCGGCATCTTTCAAAAGGACGGTGGTCTCATCCTGGGTTCAAAAGGTCAA------GTTAAAGGACCTCCAATTGAAGCCTATTGATA--CTCAGCATTGGATTCAAACCCTGCTCCGTCAAAAGCCGTGTGATCAGATCAAGAAGGTTGACCAAAGCCACAAACAAAACTACGGGGACAATCTAAATG Canine_distemper_virus_AY649446 CAAAATATCGCTATTTCCACGATGGGGCATCTATCAAGCATTATGATAGC-----TTTGGGAAGGACACTGGAGACCCTACGGCAAATGTCCAGAACTACTGGCGGAAGTTCTCAAGCAACCCGCATCATTCGGAAGGACAGCGGTATTGCCTTGGGCTCAAAAGGTCAA------ATTGAGAGACCTCCAGCTGAAACCTATTGACA--CTCGGCATCGGATACAAACCCCGCACCTTCCAAAGCTGTATGATTAGATCAAGAGAGTTGATCAAAGTCACAAACACAACTTCGGGGACAATCTAAACG Measles_virus_NC001498 CAAAATATCAGCATATCCACCCTAGGACACCTCTCAAGCATCATGATTGC-----CTTGGGAAGGATCCCAACGACCCCACTGCAGATGTCCCGACCTACTGGCCGAAGTTCTCAAGAAGCCCGTTGCCACCAGGGAATGACTAATGGACGGACCAGTTCCAGAGGACAG------GCTGAAGGAATTTCAACTAAAGCCGATCGGGA--CTCAGCGTCGGGTTTGTTCCGCCCTGCATCACGCAGTGTATTATAAAATCCAGCGGCTAGAGGAGGATCGGAAGCGTTACTCCGGAGCCGATCTTGCCA Cetacean_morbillivirus_KF711855 TCAAGGATGCTGACCTCCTCGTGGTTTCAACAGGCAGTGACAATGATGAAGCGGAGAAGAAAGCACTCCTGAGAGCGATGATGAACTTGGCCCGGAAGAAATTCTCCCTCTAACAGGAGATCTACTCCCACGAGAAGTCGTCCGATGTCGAGACAATCAGTGATGAAGAATGATAAGATCTCAGAATCTCAAGCTCAGTGGATTCAGAGGTTGATGGTTCCACCGATACCGACATCAGTGCCTCTGGATC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAATCTCAT------------------- Cetacean_morbillivirus_JX195718 ------------------------------------------------------AGATGAGAGCTCTCTCGAGAGCGATGATGAATCTTGCCCAGAGGAGATCCTCCCTCTGACAGGAGATCTGCTCCCACGAGAGAGCCTCAGATGTTGAGACTATAAGCAGTGAGGAGTGATCAGATCTCAGAACCAAAAAAGTAACAGCTTTGGGGGCTAAAAGTTCCACCAATCCCGGCCTCAGTGCCACTTGACC--ATCCATTAAAAAGGGCACAGAAGAGAA------------------------------ Pilot_whale_morbillivirus_FJ842381 ---------------TGCTCTTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGGGCGATGATGAATCTGGCCCAGAGGAGATCCTTCCTCTAACAGGGGATCTACTTCCACGAGAGATCGTCTGACGTTGAAATTATAAGTAGTGAGGATTGATCAGATCTCAGAACCAAAAGCACAATGGACTCGGAGGTTAAAGGTTCCACCAATCCCAGCATCGGTGCCTCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAAATCAGCCTCATGACCAGGTCTTCCTT---- Pilot_whale_morbillivirus_AF200817 ---------------TGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGGGCGATGATGAATCTGGCCCAGAGGAGATCCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAAATTATAAGTAGTGAGGATTGATCAGATCTCAGAACCAAAAGCACAATGGACTCGGAGGTTAAAGGTCCCACCAATCCCAACATCGGTGCCTCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAAATCAGCCTCATGACCAAGTCTTCATTGACA Porpoise_morbillivirus_KF650727 TCAAGGATGCTGACTTGCTCGTGGTTCCAACAGGCAGCGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGATGAATCTGGCCCAGAGGAGATCCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCATCCGATGTTGAGACTATAAGCAGTGAGGAATGATCAGATCTCAGAACCACAAGCAGAATGGATTCGGAGGTTAAAGGTCCCACCAATCCCGACCTCAGTACCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_EF451565 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACAGAGATGAGAGCTCTCTCGAGAGCGATGATGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGCGTCTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACT--ATCCATTAAAAAGGGCACAGGA----------------------------------- Dolphin_morbillivirus_KC888945 --------------------------CCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGATGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGAGTTGGCGTCTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACT--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTAT------------------- Dolphin_morbillivirus_KJ139453 ------------------------------CAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGAAGAGA------------------------------- Dolphin_morbillivirus_KJ139452 ------------------------------CAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAA---------------------------------------------- Dolphin_morbillivirus_JN210891 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACTTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATT---- Dolphin_morbillivirus_KF695110 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KR704575 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGACTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KR337460 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_HQ829972 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_HQ829973 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KP835995 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_EU039963 ---------------------------------GTAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAGTTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGC------------------------ Dolphin_morbillivirus_KJ139451 ------------------------------CAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAGTCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGC----------------------------------------- Dolphin_morbillivirus_AJ608288 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTCTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_AF333347 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTCGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCTGCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTCTAAAGGTCCCACCAATTCCAACCTCCGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KP835987 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTATAAGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KP835983 ---------------ACTGCTCGTGGTTCACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCCTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAAAGAGATCAGCCTTATAACCGAGTTTTCATTGACA Dolphin_morbillivirus_KP835991 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KT878657 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KC572861 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAG------------------------------ Dolphin_morbillivirus_KP835999 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATACAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KT878656 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KT878659 GTAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGGACAGGAGAAAAATCAGCCTTATGAACGAGTTTTCCTTGGCA Dolphin_morbillivirus_KT878658 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACC--ATCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KT878660 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACCA--TCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KT878661 ---AGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACCA--TCCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KP836003 TCAAGGATGCTGACCTGCTCGTGGTTCCAACAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAACCTCAGTGCCGCTGGACCAATCTCATTAAAAAGGGCACAGGAGAGAGATCAGCCTTATGACCGAGTTTTCATTGACA Dolphin_morbillivirus_KJ139454 ------------------------------CAGGCAGTGATGATGATGCAACGGAGATGAGAGCTCTCTTGAGAGCGATGGTGAATCTGGACCAGAGGAAATTCTTCCTCTAACAGGGGATCTGCTCCCACGAGAGATCGTCTGACGTTGAGACTATAAGCAGTGAAGAGTGATTAGATCTCAGAGTCAAAAACATAATGGATTTGGAGTTTAAAGGTCCCACCAATTCCAAC---------------------------------------------------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = P_gene_alignment) = unord: 1 - 309; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = P_gene_alignment) = universal: 1 - 309; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = P_gene_alignment) = 'Jukes-Cantor': 1 - 309; END; BEGIN TREES; Title P_gene_tree; LINK Taxa = P_gene; TRANSLATE [0] n0 Phocine_distemper_virus_KC802221, [1] n1 Canine_distemper_virus_AY649446, [2] n2 Measles_virus_NC001498, [3] n3 Cetacean_morbillivirus_KF711855, [4] n4 Cetacean_morbillivirus_JX195718, [5] n5 Pilot_whale_morbillivirus_FJ842381, [6] n6 Pilot_whale_morbillivirus_AF200817, [7] n7 Porpoise_morbillivirus_KF650727, [8] n8 Dolphin_morbillivirus_EF451565, [9] n9 Dolphin_morbillivirus_KC888945, [10] n10 Dolphin_morbillivirus_KJ139453, [11] n11 Dolphin_morbillivirus_KJ139452, [12] n12 Dolphin_morbillivirus_JN210891, [13] n13 Dolphin_morbillivirus_KF695110, [14] n14 Dolphin_morbillivirus_KR704575, [15] n15 Dolphin_morbillivirus_KR337460, [16] n16 Dolphin_morbillivirus_HQ829972, [17] n17 Dolphin_morbillivirus_HQ829973, [18] n18 Dolphin_morbillivirus_KP835995, [19] n19 Dolphin_morbillivirus_EU039963, [20] n20 Dolphin_morbillivirus_KJ139451, [21] n21 Dolphin_morbillivirus_AJ608288, [22] n22 Dolphin_morbillivirus_AF333347, [23] n23 Dolphin_morbillivirus_KP835987, [24] n24 Dolphin_morbillivirus_KP835983, [25] n25 Dolphin_morbillivirus_KP835991, [26] n26 Dolphin_morbillivirus_KT878657, [27] n27 Dolphin_morbillivirus_KC572861, [28] n28 Dolphin_morbillivirus_KP835999, [29] n29 Dolphin_morbillivirus_KT878656, [30] n30 Dolphin_morbillivirus_KT878659, [31] n31 Dolphin_morbillivirus_KT878658, [32] n32 Dolphin_morbillivirus_KT878660, [33] n33 Dolphin_morbillivirus_KT878661, [34] n34 Dolphin_morbillivirus_KP836003, [35] n35 Dolphin_morbillivirus_KJ139454; TREE con_50_majrule = (((n3:0.1948205,n4:0.1121531,(n5:0.02146434,n6:0.002103609):0.05747999,n7:0.02598499,(((n8:0.005156616,n9:0.005003257):0.01305811,n21:0.001849755,n22:0.01487368):0.00447712,n20:0.005537395,(n10:0.006037569,((n12:0.004671078,n13:0.002976969,n14:0.00461062,n15:0.001963518,n16:0.001970944,n17:0.001776586,n18:0.001833283,n19:0.002454751):0.004615215,n11:0.004022021):0.004556898):0.004313918,(n23:0.007291554,n24:0.04592826,n25:0.004169478,n26:0.00181079,n27:0.001972075,n28:0.004602669,n29:0.001749245,n30:0.02194095,n31:0.001778094,n32:0.001779146,n33:0.001700646,n34:0.01172715,n35:0.00274247):0.007362264):0.04310553):1.467708,(n0:0.1560681,n1:0.1245549):0.5258196):0.049943955,n2:0.049943955); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1467109791665; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 46177308466308728; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3376220300185172346; mqVersion 304; checksumv 0 3 3451003493 null getNumChars 309 numChars 309 getNumTaxa 36 numTaxa 36 short true bits 15 states 15 sumSquaresStatesOnly 203841.0 sumSquares 203841.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1354 649; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #46177308466308728 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #46177308466308728; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1254 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #46177308466308728 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 948.1467042058912.619694968669840910; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1254 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.interchange; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3376220300185172346 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1254 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;