#NEXUS [written Tue Apr 22 17:02:17 CEST 2014 by Mesquite version 2.74 (build 550) at PC-Alberto/161.111.161.177] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Mus_m._musculus Mus_m._castaneus Mus_m._domesticus Mus_m._bactrianus Mus_macedonicus Mus_spicilegus Mus_spretus Mus_famulus Mus_cokii Mus_caroli Mus_pahari Mus_minutoides Mastomys_natalensis Apodemus_sylvaticus Lemniscomys_barbarus Rattus_norvegicus ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=1080; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Mus_m._musculus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCCCACCCCCACCCTACCCTGCGTAGGCCAAGCCAAGGTGGCGTCTAT---TACGATTCTCCTCAGCATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAATAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACCATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCAT---------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTTCTATCGC---------TCCCATGCGCCGTTCAGTCGCCAGGAAAGACCTCATCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------TTCTCACCATGGTGAACAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCATCAC------CATATCCATCATCG---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACACTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCGCTCTCAAATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_m._castaneus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCCCACCCC------ACCCTGYGTAGGCCAAGCCAAGGTGGCGTCTAT---TACGATTCTCCTCAGCATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAATAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACCATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCAT---------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTTCTATCGC---------TCCCATGCGCCGTTCAGTCGCCAGGAAAGACCTCATCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------TTCTCACCATGGTGAACAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCATCAC------CATATCCATCATCG---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACACTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCGCTCTCAAATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_m._domesticus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCCCACCCC------ACCCTGYGTAGGCCAAGCCAAGGTGGCGTCTAT---TACGATTCTCCTCAGCATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAATAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACCATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCAT---------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTTCTATCGC---------TCCCATGCGCCGTTCAGTCGCCAGGAAAGACCTCATCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------TTCTCACCATGGTGAACAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCATCAC------CATATCCATCATCG---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACACTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCGCTCTCAAATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCAYGTT Mus_m._bactrianus ATGGATCAATCTTCGAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACACTGCATAGGCCAAACCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCACACCAACAGCATGGTGGGTTCCATCAGCAAAATGAATTTCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCCGGTGTCTCTACCTTACCTAGTAACATCCCTCACGCTTATAGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCATATTGACCCGAATCATCGTCCCCACCAAGCTGACCCCCGTAGACCCAGTGAACCTTTGTCCCACCTCCTCTCTACTGGCACCCACCAAGGGACAACCCATCAACAACACTTTGAGAGGTCTCAACATCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACAACATTTCCTATCGCTCCAGTACGCGGTCCCATCGC---------TCCACTGCGCCGTCCAGTCGCCAGGAAAGACCTCACCTCCACGCTAATC------------------------ACCATCATGAGGGCCATCATGCCCA------CTCTCACCGTGGTGAGCAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCAGCGC------CATATCCATCATCA---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCAACTTTGGAGCTCGCTCTCATATTTTCGGGCAAAGAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTCTGAGTGAAGGGGAGGATCACGTT Mus_macedonicus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACCCTGCGTAGGCCAAACCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAGTAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACTATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTCCTATCGC---------TCCAATTCGCCGTTCAGTCGCCAGGAAAGACCTCACCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------TTCTCACCATGGTGAACAT------------------------------------------------------------CCCCATCACAAGGAGCAAAGGCACTATCAG------GGAGATCATACGCATCAC------CATATCCATCATCG---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCGCTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_spicilegus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACCCTGCATAGGCCAAGCCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAGTAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACTATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTCCTATTGC---------TCCAATTCGCCGTTCAGTCGCCAGGAAAGACCTCACCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCG------TTCTCACCATGGTGAACAT------------------------------------------------------------CCCCATCACAAGGAGCAAAGGCACTATCAG------GGAGATCATACGCATCAC------CATATCCATCATCG---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCGCTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_spretus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCCCACCCC------ACCCTGYGTAGGCCAAGCCAAGGTGGTGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTGCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCTGGTGTCTCTACCTTACCTAGTAACATCTCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCGTATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAATACTATGAGAGGTCTCACCATCTTAACCCCCAGCAGAACAGAGATCATCAT------GCAGACACCATTTCCTTTCGCTCCAGTACGCGGTCCTATCGC---------TCCAATGCGCCGTTCAGGCACCAGGAAAGACCTCACCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------TTCTCACCATGGTGAACAT------------------------------------------------------------TCCCATCACAAGGAGCAACGGCACTATCAC------GGAGATCATACACATCAC------CATATCCATCATCA---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGTCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAGCTCACTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_famulus ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACCCTGCATAGGCCAARCCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTTCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCCGGTGTCTCTACCTTACCTAGTAACATCCCTCACGCTTATGGTGGATTGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCACATTGACCCGAATCATCATCCCCACCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCAACAACACTATGAGAGGTCTCACCAKCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACACCATTTCCTATCGCTCCAGTACGAGGTCCCATCGC---------TCCATTGCGCCGTTCAGTCGACAGGAAAGACCTCACCTCCAAGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------CTCTCACCATAGTGAACAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCGCTATCAC------GGAGATCAT------CAC------CATATCCATCATCA---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCACCTTTGGAACTCGCTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mus_cokii ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACACTGCATAGGCCAAACCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCACACCAACAGCATGGTGGGTTCCATCAGCAAAATGAATTTCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCCGGTGTCTCTACCTTACCTAGTAACATCCCTCACGCTTATAGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCATATTGACCCGAATCATCGTCCCCACCAAGCTGACCCCCGTAGACCCAGTGAACCTTTGTCCCACCTCCTCTCTACTGGCACCCACCAAGGGACAACCCATCAACAACACTTTGAGAGGTCTCAACATCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACAACATTTCCTATCGCTCCAGTACGCGGTCCCATCGC---------TCCACTGCGCCGTCCAGTCGCCAGGAAAGACCTCACCTCCACGCTGATC------------------------ACCATCATGAGGGCCATCATGCCCA------CTCTCACCGTGGTGAGCAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCAGCGC------CATATCCATCATCA---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCAACTTTGGAGCTCGCTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAGAGAATCAGCCTCTCTGAGTGAAGGGGAGGATCACGTT Mus_caroli ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTAGACCCAAGCCATCAATCCCA---------------------CCCCCACCCCCACCCC------------ACCCTGCATAGGCCAAACCAAGGTGGCGTCTAT---TACGATTCTCCTCAACATGGGATGTTCCAACAACCATACCAACAGCATGGTGGGTTCCATCAACAAAATGAATTTCAGCATTTGCGTGAGTTCTCAGACTCCCATGACAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCCGGTGTTTCTACCTTACCTA---ACATCCCTCACGCTTATGGTGGATCGCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCATATTGACCCGAATCATCATCCCCACCAAGCTGACCCCCGTAGACCCAGTGAACCTTTGTCCCACCCCCACTCTACTGGCACCCACCAAGGGACAACCCATCAACAACACTTTGAGAGGTCTCAACATCTTAACCCCCAGCAGAACAGAGATCATTAT------GCAGACACCATTTCCTATCGCTCCAGTACGCGGTCCCATCGC---------TCCATTGCGCCGTTCAGTCACCAGGAAAGACCTCGCCTCCACGCTGATCCCCATCATGAGGGCCGTCATGAGGGCCATCATGAGGGCCATCATGCCCA------CTCTCACCATGGTGAGCAT------------------------------------------------------------CCCCACCACAAGGAGCAACGGCACTATCAC------GGAGATCATATGCAGCGC------CATATCCATCATCA---CTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACCTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCAACTTTGGAGCTCATTCTCATATTTTCGGC---AAAGCTCAGTCCAGGGAGAGCTTGAAAGAATCAGCCTCTCTGAGTGAAGGGGAGGATCACGTT Mus_pahari ATGGATCAATCTTCAAGGAGGGACGAGTCTTACCATGAGACACACCCCGGTAGCTTCGACCCAAGCCATCAATTCCAGCCATCATCCTCTCACCCCAACCCCCATCCCCACCCCCATCCC------ACCCTGTGTAGGCCAAGCCAAGGTGGCGTCTAT---TATGATTCTCCTCAACATGGGATGTTACAACAACCATACCAACAGCATGGTGGGGTCCATCAACAAAATGAATTCCAGCATTTGCGTGAGTTCTCAGACTTCCATGATAATGCTTTCTCCCATCATTCCTATCAGCAG---GACAGGGCCGGTGTCTCTACATTACCTAGTAACATCCCTCACGCTTATGGTGGAGCTCACCCCCTTGCTGAGTCTCAGCACTCTGGTGGACCCCAGAGTGGACC---------------------TCCCCACCAAGATGATCCCCATAGACMCAGTGAACYTTTGTCCCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACCCATCGACA---CCATGAGAGGCTTCACCATCTTAACCCCCAGCAGGACAGAGATCAATCTCAACAGGCAGACACCATTTCCTATCGCTCCAATACGCGGCCCTATCGC---------TCCAATGCGCCA---AGTCGCCAGGAAAGAC---GCCTCCAAGCTGATT------------------------CCCAGCATGAGGGCCAGCGCGCCCA------CTCTCACCGTGGTGAGCGTGATGAGCAT---------------------------------------------------CCCCACCACAGGGAGCAACGACACTATCACTATCACGGAGATCATATGCAGCGCAGAGAACGTATCCATCATCATCGCTCCCCAAGTGCCTCCCAACTCTCACACAAGTCTCACAGCACAGTTGCCACTTCTCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCGTCTTTGGAGGTCGCTCTCATGTTTTCAGC---AAAACTCAGTCCAGGGAGAGCTTGAGAGAATCGGCTTCTTTTAGTGAAGGGGAGGATCACGTT Mus_minutoides ATGGATCAATCTTCAAGGAGGGACGAGGCTTACTATCAGACACACTCCGGTAGCTTAGACCCAAGCCCTCAATTCCAGCCATCACC------------CCCCCACCCCCACCTCCACCCCCACCCCACCCTGCATAGGCCAAACCAAGGTGGCGTCTAT---TATGATTCCCCTCAACATGGGATGTTCCAACAGCCATACCAACAGCATGGTGGGTTCCATCCACAAAATGAATTCCAGCATGTGCGTGAGTTCTCAGACTTCCATGACAATGCTTTCTCCCATTATTCCCATCAGCAG---GACAGGGCCGGTGTCTCTACCTTACCTAGTAACATCCCTCACGCTTATGGTGGGTCTCACCCCCTTGCTGAGTCCCAGCACTCTGGTGGACCCCAGAGTGGACCTCATATTGACTCGAATCATCATCCCCATCAAGATGACCCCCATAGACCCAGTGAACCTTTGTCTCACCCCTCCTCTACTGGCAGCCACCAAGGGACAACTCATCAACA---CTATGATAGGTCTGACTATCTTAACCTCCAGAAGAACAGAGAACACCAT------GCAGACGCCATTTCCTATCGCTCCAATCCGCGGTCATATCG---------------------------TCACCATGGAAGGCCTCGCCCCACAGCTGATC------------------------CCCAGCATGAGGGCCAGCACGCCCATGCTCACGCTCACCGTGGTGAGCGTGGTGAGCAT---------------------------------------------------CCCCACCACAGG------------------------GAGCATCATATGCAGCGC------CGTATCCATCATCA---CTCCCCAAGTACCTCCCAATTCTCACACAAGTCTCACAGCACACTTGCCACCTCGCCATCTCATGTGGGATCGAAAAGCACAGCCAGTGGGGCTCGGTCCGCCTTAGGAATTCGCTCTCGTATTTTCGGC---AAAGCTCAGTCCAGTGAGAGCTTGAAAGAATCAGCCTCTTTGAGTGAAGGGGAGGATCACGTT Mastomys_natalensis ATGGATCAACCTTCAAGGAYGGGCGAGTCTTTCCACGAGACACACCCCGGAGGCTTAGATCCAAGCCATCACTTCCACCCATCATCCTCCCATCCCTACCCTCACCTCTACCCTCATCTCCACCCCACCCTGCGTAGGCCAAGCCACAGTGGTGTCCAT---TATGATTCTCCTCAACATGGGATGTTCCAACAATCACCCCAACATCATGCTGGGTTCCCTCAACAAAATGAATCCCAGCATTTGCGTGAGTTCTCAGACTTCCATGAGAGTGCCATCTCCCATCATTCCTATCAGCAG---GACAGGGCCCATCTCTCCATATTACCTAGCAATATCCCTCAGGCTTATGGTGGATCTCATCCTCCTGGTGAGTCTCAACACTCTGGTGGACCCCAGAGTGGATCTCTTATTGACCCACATCATCATCCCCACCAAGATAACTT---TAGAGCCAGTATAGTTTTGCC---------------------CCGCCATGGGACAACCCA---------CTATGAGAGGTCTGACCATCTTGACCAGCAGCAGAACAGAAGGCAGTCTCAGAATGCAGAAAACATTTCCCATCACTCCAATGCACCGTCCCAACGCCAGGAAGGATCTCACCATCAAGTTGACCATCCTGGGGGCCATCAAGCCCACTCTCACC---------------------------------------------------------------GTGGTGAGCATGGTGAGCATGGTGAGCATGGTGAGCATGGTGAGCATGGTGAGCATGGTGAGCATGGTGAG---CACCACAGGGAGCAACGACATCATCGT------GGAGGTCACATGCAGCAC------CGTTTACATCATCG---CACCCCAAGTGTCTCCCAACTCTCACACAAGTCCCACAGCACAGTTGTCACCACTCATTCTCATGCAGGCTCCAAAAGCACAACCAGTAGGCCTCGTTCCATCTTGGGAGCTCGATCCCATGTTTTCAGC---CAAGTTCATTCCAAGGAGAGCTTGAGAGAATCACCCTCTTTGAGCGGAGAGGAGGATCATGTT Apodemus_sylvaticus ATGGATCAACCTTCAAGGAYGGGCGAGTCTTTCCACGAGACACACCCCGGTAGCTTAGATCCAAGCCATCACTTCCACCCATCATC------------CTCCCACCCTCAACCCCACCCC------ACCCTGCGTAGGCCAAGCCGCAGTGGCGTTCAT---TATGAGTCTCCTCAACATGGGACGTTCCAACAACCATCCCAACAGCATGCTGGGTTCCATCAACAAAATGAATCCCAGCATTTGCGTGAGTTCTCAAACTTCCATGATAGTGCTTTCTCCCATCATTCCCATCAGCAG---GACAGGGCCCATTTTGCCACATTACCTAGTAATACCCCTCATGCCTATGCTGGCTCTCACCCAGTTGCTGAGTCTCAGCAGTCTGGTGGACCCCA---------------------------TCCTTCCCACCAAGATGACCCTCCTAGACCCAGTGAAGCTATGTCCCAACCCTCCTCTGCTGGCGGCCGCTATGCTCAACCTCACCA------CCATGAGAGGCCTCACCATCTTGACCCCCAGCAGAACAGAAGGCAGTCTCAACTTTCAGAGAACATTTCCCATCGCTCCATGGAAAGATCTCGCTCC------------------CCAGCTGATCATCATGAGGGCCATCGAGTCCATGGCGATC---------------------------------------AGCG------------CTCT---------GAGCGGGGTGAGCGT---------------------------------------------------CACCACCACAGGGAGCAACGACACCATCGT------GGAGATCGTGTGCATCACAGAGACCGTTTCCACCATCG---CTCCCCAAGCATCTCCCAAGTCTCACACAAGTCCCACAGCACAGTTGCCACCTCTCCTTCTCATGTGGGATCCAAAAGCACAGCCAGCGGGGCTCGGTCCTACTTTGGAACTCGATCTCGAATTTTCGGC---AAAGTTCATTCCAGGGAGAGCTTGAAAGAATCG---TCTTTGAGTGAAGGGGAGGATCATGTT Lemniscomys_barbarus ATGGATCAACCTTCAAGGACAGATGAGTCTTACTATCAGAGACACTCGGGTAGCTTAGATCCAAGCCATCACTTCCACCCACCATCTTCCCA------CCCCCACCCCCACCCCCACCCC------ACACCGCATAGGCCAAGTTACAGTGGCTTTCAT---CATGAGTCTCCTCAACATGGGATGTTCCAACAACCATCCCAACAGCATGCTGGGTTCCATCAACAAAATGAATCCCAGCATTTGCGTGAGTTCTCAGACTTCCATGACAGTGCCTTATCCCATCATTCCTATCAGCAGCAGGACAGGGCCCGTGTTTCCACATTACCTAGTAATGTCCCTCGTGCTTATGGTGGATCTCACCCCGTTGCTGAATCTCAGCACTCTGGTGGACCCCAGAGTGGTTCTCATATTGAACCCTCTCATCATTCCTACCAAGATGAACCCCGTAGACCCAGTGAAGCTTTGTCCCAGCCC---TCTACTGGCACCCGTTATGTAAGAACCCATCACCA---CAATGAGAGGCCTCAACATCTTGACCCTCAGCAGAACAGACGGCAGTCTGATCATGCAGACAACATCTCCCATCGCTCAGAGATGGAG---------------------------------CATCACCATGAAAGATCTCGCGTCCACGCTGATT------------------------CCCACCAGGCAGGCCACAAAGCTCG-------------------------------------------------------------------------------------------CCAAGGGAGCAACGACGCCATCAT------GGAGATCGTACGCTCCATAGAGAACATATCCACCATCG---TGTCCCAAGCACCTCCCAGCTCTCACACAAGTCCCACAGCACCATCGCCACCTCTCCTTCTCATGTGGGATCCAAAAGCACAGCCAGTGGAGCACGGTCCTTCTTGAGAGCTCGATCTCAGGCCTCCGGC---AGAGTTCATTCTAAGGACAGCTTGAAAGAATCAGTCTCTTGGAGTGACGAGGAG---CACGTT Rattus_norvegicus ATGGATCAACCTTCAAGGACAGACGAGTCTTACTATGAGACACACTCTGGTAGCTTGGATCCAAGCCATCACTTCCACCCACCATCCTCCTACCCCTATCCCCACCCC------------------ACACTGTATAGGCCAAGCCTCGGTGGAGTCCTTCATCATGAGTCTCCTCAACATGGGGTGTCCCCACAACCATCCCAACAGCATGCTGGATTCTATCAACAAAATGAATCCCAGCATTTGCGTGGAT---CAGACTTCCATGATAGTGCTTTCCCCCATCATTCCTATCATCAG---GACAGGGCCCACTTCTCCACATCACCTACTAATGTCCCTCACACTTATGGCGGACCTCATCCCCTTGCTGAGTCTCAGCACTCTGGTGGACCCCAAGATGGATCTCATATTGAATCCTATCAT---TCCCACCAAGGTAACCCCCGTAAACCCAGTGTAGCTTTGTCCCATCCCTCCTCTATTGGCAGCCACCAAGGGAAAACCCATCACCA---CTATGAGAGGCCTCAATATCTTGACCCTCGCCAGAGCAGAAGGCAGTCTGACCTTTCAGACAACCTTTCCCATCGCTCTGGTGAGGAGTAC------------------------------CAAAACCAGGAAAGATCTGGTCTCCAAGTCGGTC------------------------AGCAACAGGAGGGCCAGCGAGCCAG------CTCTAAACGTGGTGAGCAT------------------------------------------------------------------------------CGACGCCGGCGT------GGAGATTATTTGAAGTACAAAGACCGTATTCGCCATCG---CCGCCCAAGTGCTTCCCAGCTCTCACACAAGTCCCACAGCACAGAAGGCACCTCTCCTTCTCATATGAGATCCAAGAGCTTAGCCAGTATGCCTCAGTCTCACTTGGGAGTTCAATCTTATGTTTCCAGC---CAAGTTCATTCCGGGGATAGCTTGAAAGAATCAGTCTCTTGGAGCGATGAGGAC---CATGTT ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1080; END; BEGIN TREES; Title 'Catsper1_Neighbour_Joining_Tree'; LINK Taxa = Taxa; TRANSLATE 1 Mus_m._musculus, 2 Mus_m._castaneus, 3 Mus_m._domesticus, 4 Mus_m._bactrianus, 5 Mus_macedonicus, 6 Mus_spicilegus, 7 Mus_spretus, 8 Mus_famulus, 9 Mus_cokii, 10 Mus_caroli, 11 Mus_pahari, 12 Mus_minutoides, 13 Mastomys_natalensis, 14 Apodemus_sylvaticus, 15 Lemniscomys_barbarus, 16 Rattus_norvegicus; TREE 'Catsper1_Neighbour_Joining_Tree' = ((((((((((2:0.0,3:0.0):0.0,1:0.0):0.00731106,5:-1.9153E-4):8.718E-4,6:5.6394E-4):0.00126289,7:0.00869114):0.00543502,(10:0.0068805,(4:0.00664245,9:-9.6041E-4):0.00962918):0.00865036):7.6664E-4,8:0.00651166):0.00532313,12:0.09095692):0.01397859,11:0.03256021):0.10617646,(13:0.16800572,14:0.10647075):0.02062227,(15:0.12058965,16:0.22644872):0.05535202); END; BEGIN TREES; Title 'Catsper1_Maximum_Likelihood_Tree'; LINK Taxa = Taxa; TRANSLATE 1 Mus_m._musculus, 2 Mus_m._castaneus, 3 Mus_m._domesticus, 4 Mus_m._bactrianus, 5 Mus_macedonicus, 6 Mus_spicilegus, 7 Mus_spretus, 8 Mus_famulus, 9 Mus_cokii, 10 Mus_caroli, 11 Mus_pahari, 12 Mus_minutoides, 13 Mastomys_natalensis, 14 Apodemus_sylvaticus, 15 Lemniscomys_barbarus, 16 Rattus_norvegicus; TREE 'Catsper1_Maximum_Likelihood_Tree' = ((((((((((2:0.0,3:0.0):0.0,1:0.0):0.00714156,7:0.0099864):0.00140965,5:0.0):0.00140974,6:0.0):0.00588158,(10:0.00852099,(4:0.00568225,9:0.0):0.00721059):0.00857371):0.00142022,8:0.00588647):0.01457708,12:0.06884822):0.00813544,11:0.02837589):0.07515361,(13:0.12487046,14:0.07973853):0.01993406,(15:0.09125735,16:0.14644717):0.02758996); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 1080; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1080; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1398178937215; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8033095569431821841; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6094616351583315545; mqVersion 274; checksumv 0 2 449818459 null getNumChars 1080 numChars 1080 getNumTaxa 16 numTaxa 16 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 270609.0 sumSquares -6.456360425798342E19 NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 140; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 903 500; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8033095569431821841 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8033095569431821841; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; 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.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; showTrees 1 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 2; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1011.1398176470724.7960698593418484380; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1044.1398177089227.1163196552585842324; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.NodeNamer.NodeNamerExtra.nodeNamer; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1082.1398178437160.1389826294091921147; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1113.1398178484720.1013891975945924261; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1150.1398178695246.4046251090234130413; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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; makeTreeWindow #8033095569431821841 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 2; toggleUseWeights off; endTell; setAssignedID 1181.1398178741050.3206633972546405185; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; 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 on; toggleHorizontal 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 #6094616351583315545 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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; 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; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; showCharacters #6094616351583315545 #mesquite.lists.CharacterList.CharacterList; tell It; setData 0; getWindow; tell It; newAssistant #mesquite.lists.CharListInclusion.CharListInclusion; newAssistant #mesquite.stochchar.CharListProbModels.CharListProbModels; newAssistant #mesquite.lists.CharListCodonPos.CharListCodonPos; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 763 433; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; endTell; end;