#NEXUS [written Mon Jun 11 15:51:30 CEST 2018 by Mesquite version 3.04 (build 725) at Macintosh.local/10.10.30.245] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=25; TAXLABELS Ochrolechia_szatalaensis Ochrolechia_upsaliensis Ochrolechia_subviridis_1 Ochrolechia_subviridis_2 Ochrolechia_subviridis_3 Ochrolechia_parella_1 Ochrolechia_parella_2 Ochrolechia_parella_3 Ochrolechia_parella_4 Ochrolechia_parella_5 Ochrolechia_parella_6 Ochrolechia_parella_7 Ochrolechia_parella_8 Ochrolechia_parella_9 Ochrolechia_parella_10 Ochrolechia_parella_11 Ochrolechia_parella_12 Ochrolechia_parella_13 Ochrolechia_parella_14 Ochrolechia_parella_15 Ochrolechia_parella_16 Ochrolechia_incarnata_1 Ochrolechia_incarnata_2 Ochrolechia_incarnata_3 Ochrolechia_incarnata_4 ; END; BEGIN CHARACTERS; TITLE Ochrolechia_incarnata_Alignment; DIMENSIONS NCHAR=541; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Ochrolechia_szatalaensis ?????????????????????????CCGA-G-AGAGGGTCC-TTCGGGGC Ochrolechia_upsaliensis ???????CCTGCGGAAGGATCATTACCGA-G-AGAGGGTCCCTTTGGGGC Ochrolechia_subviridis_1 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TTCAGGGC Ochrolechia_subviridis_2 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TTCGGGGC Ochrolechia_subviridis_3 ??????ACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TTCGGGGC Ochrolechia_parella_1 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_2 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_3 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_4 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_5 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_6 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_7 ????????????????????CATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_8 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_9 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_10 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_11 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_12 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_13 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_14 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_15 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_parella_16 AGGTGAACCTGCGGAAGGATCATTACCGA-GAAGAGGGTCC-TCCGGGGC Ochrolechia_incarnata_1 AGGTGAACCTGCGGAAGGATCATTACCGA-GGAGAGGGTCCCTT-GGGGC Ochrolechia_incarnata_2 ?????????TGCGGA-GGATCATTACCGA-GGAGAGGGTCCCTT-GGGGC Ochrolechia_incarnata_3 AGGTGAACCTGCGGAAGGATCATTACCGA-GGAGAGGGTCCCTT-GGGGC Ochrolechia_incarnata_4 ???????CCTGCGGAAGGATCATTACCAAAGTAGAGGGTCCCTT-GGGGC Ochrolechia_szatalaensis CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_upsaliensis CCGACCCTCCCATCCCCTGTGTATGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_subviridis_1 CCGACACTCCCATCCCGTGTATACGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_subviridis_2 CCGACACTCCCATCCCGTGTATACGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_subviridis_3 CCGACACTCCCACCCCGTGTATACGTGCCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_parella_1 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_2 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_3 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_4 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_5 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_6 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_7 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_8 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_9 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_10 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_11 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_12 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_13 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_14 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_15 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_parella_16 CCGACCCTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCC- Ochrolechia_incarnata_1 CCGACCTTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGTGGGCCCG Ochrolechia_incarnata_2 CCGACCTTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGTGGGCCCG Ochrolechia_incarnata_3 CCGACCTTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_incarnata_4 CCGACCTTCCCATCCCGTGTGTACGTACCTCTGTTGCTTCGGCGGGCCCG Ochrolechia_szatalaensis TGGGTCCCTTTGGGGCTCACCACCGGCGTCGGTCGGTCCGCGCCCGCCAG Ochrolechia_upsaliensis TGGGTCCCTTTGGGGCTCACCACCGGCGTCGGTCGGTCCGCGCCCGCCAG Ochrolechia_subviridis_1 TGGGTCCTCCTGGGACTCACCGCCGGCATCGGTCGGTCCGCGCCCGCCAG Ochrolechia_subviridis_2 TGGGTCCTCCTAGGACTCACCGCCGGCATCGGTCGGTCCGCGCCCGCCAG Ochrolechia_subviridis_3 TGGGTCCTCCTGGGACTCACCGCCGGCGTCGGTCGGTCCGCGCCCGCCAG Ochrolechia_parella_1 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_2 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_3 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_4 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_5 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_6 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_7 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_8 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_9 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_10 ---------------------------------------GTACCCGCCAG Ochrolechia_parella_11 --------------------------------------CGTACCCGCCAG Ochrolechia_parella_12 --------------------------------------CGTACCCGCCAG Ochrolechia_parella_13 --------------------------------------CGTACCCGCCAG Ochrolechia_parella_14 --------------------------------------CGTACCCGCCAG Ochrolechia_parella_15 --------------------------------------CGTACCCGCCAG Ochrolechia_parella_16 --------------------------------------CGTACCCGCCAG Ochrolechia_incarnata_1 TGGGCCCTTCGGGGGCTCACCGCCGGCGTCGGTCGGCCCGCGCCCGCCAG Ochrolechia_incarnata_2 TGGGCCCTTCGGGGGCTCACCGCCGGCGTCGGTCGGCCCGCGCCCGCCAG Ochrolechia_incarnata_3 TGGGCCCTTCGGGGGCTCACCGCCGGCGTCGGTCGGCCCGCGCCCGCCAG Ochrolechia_incarnata_4 TGGGCCCTTCGGGGGCTCACCGCCGGCGTCGGTCGGCCCGCGCCCGCCAG Ochrolechia_szatalaensis AGGCCC-CACC-AAACCCGACTGTGCCAGTGAGGTCTGAGTGCAACGCAA Ochrolechia_upsaliensis AGGCCCTTATC-ACACCCGATTGTGCCAGTGAGGTCTGAGTGCAACGTAA Ochrolechia_subviridis_1 AGGCCCTCATC-AAATCCGCTTGCATCAGTAGAGTCTGAGTGCAACGCAA Ochrolechia_subviridis_2 AGGCCCTCATC-AAATTCGCTTGCATCAGTAGAGTCTGAGTGCAACGCAA Ochrolechia_subviridis_3 AGGCCCTCATC-AAATCCGCTTGCATCAGTAGAGTCTGAGCGCAACGCAA Ochrolechia_parella_1 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_2 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_3 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_4 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_5 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_6 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_7 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_8 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_9 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_10 AGGCCCTCACCCAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_11 AGGCCCTCACCAAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_12 AGGCCCTCACCAAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_13 AGGCCCTCACCAAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_14 AGGCCCTCACCAAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_15 AGGCCCTCACCAAAACCCGATTGTATCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_parella_16 AGGCCCTCACCAAAACCCGATTGTACCAGTGAGGTCTGAGTGTATCGCAA Ochrolechia_incarnata_1 AGGCCCTCATC-AAACCCGATTGTGCCAGTGGAGTCTGAGTGCAACGCGA Ochrolechia_incarnata_2 AGGCCCTCATC-AAACCCGATTGTGCCAGTGGAGTCTGAGTGCAACGCGA Ochrolechia_incarnata_3 AGGCCCTCATC-AAACCCGATTGTGCCAGTGGAGTCTGAGTGCAACGCGA Ochrolechia_incarnata_4 AGGCCCTCATC-AAACCCGATTGTGCCAGTGGAGTCTGAGTGCAACGCGA Ochrolechia_szatalaensis TACAGTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_upsaliensis TACAGTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_subviridis_1 TAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_subviridis_2 TAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_subviridis_3 TAAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_1 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_2 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_3 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_4 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_5 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_6 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_7 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_8 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_9 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_10 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_11 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_12 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_13 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_14 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_15 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_parella_16 TGAACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_incarnata_1 TGAACGAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_incarnata_2 TGAACGAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_incarnata_3 TGAACGAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_incarnata_4 TGAACGAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGA Ochrolechia_szatalaensis ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_upsaliensis ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_subviridis_1 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_subviridis_2 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_subviridis_3 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_1 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_2 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_3 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_4 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_5 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_6 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_7 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_8 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_9 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_10 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_11 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_12 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATCCAGTGAATCAT Ochrolechia_parella_13 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_14 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_15 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_parella_16 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_incarnata_1 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_incarnata_2 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_incarnata_3 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_incarnata_4 ACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCAT Ochrolechia_szatalaensis CGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT Ochrolechia_upsaliensis CGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT Ochrolechia_subviridis_1 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_subviridis_2 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_subviridis_3 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_1 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_2 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_3 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_4 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_5 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_6 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_7 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_8 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_9 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_10 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_11 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_12 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_13 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_14 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_15 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_parella_16 CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCGAGGGGCATGCCT Ochrolechia_incarnata_1 CGAATCTTTGAACGCACATTGCGCCCTTCGGTATTCCGAGGGGCATGCCT Ochrolechia_incarnata_2 CGAATCTTTGAACGCACATTGCGCCCTTCGGTATTCCGAGGGGCATGCCT Ochrolechia_incarnata_3 CGAATCTTTGAACGCACATTGCGCCCTTCGGTATTCCGAGGGGCATGCCT Ochrolechia_incarnata_4 CGAATCTTTGAACGCACATTGCGCCCTTCGGTATTCCGAGGGGCATGCCT Ochrolechia_szatalaensis GTTCGAGCGTCATTACACCTCTCAAGCTTGGCTTGGTGTTGGGTCCCGTC Ochrolechia_upsaliensis GTTCGAGCGTCATTACACCTCTCAAGCTTAGCTTGGTGTTGG-CCCCGTC Ochrolechia_subviridis_1 GTCCGAGCGTCATTACGCCTCTCAAGCTTGGCTTGGTCTTGGGACCCGTC Ochrolechia_subviridis_2 GTCCGAGCGTCATTACACCTCTCAAGCTTGGCTTGGTCTTGGGACCCGTC Ochrolechia_subviridis_3 GTCCGAGCGTCATTACACCTCTCAAGCTTGGCTTGGTCGTGGGACCCGTC Ochrolechia_parella_1 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_2 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_3 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_4 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_5 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_6 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_7 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_8 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_9 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_10 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_11 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_12 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_13 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_14 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_15 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_parella_16 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_incarnata_1 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCGTGGGCCCCGTC Ochrolechia_incarnata_2 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCGTGGGCCCCGTC Ochrolechia_incarnata_3 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_incarnata_4 GTCCGAGCGTCATTACACCTCTCAAGCTCGGCTTGGTCTTGGGCCCCGTC Ochrolechia_szatalaensis CTCCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCACCAGGCTTCAAGCG Ochrolechia_upsaliensis CTCCGCGGGCGGGTCCGAAAGTCAGTGGCGGTGCCACCGGGCTTCAAGCG Ochrolechia_subviridis_1 CTTCGCGGGCGGACCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_subviridis_2 CTTCGCGGGCGGACCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_subviridis_3 CTCCGCGGGCGGACCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_parella_1 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_2 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_3 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_4 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_5 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_6 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_7 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_8 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_9 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_10 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_11 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_12 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_13 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_14 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_15 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_parella_16 CTTCGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGCCGGGCTTCAAGCG Ochrolechia_incarnata_1 CTTTGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_incarnata_2 CTTTGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_incarnata_3 CTTTGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_incarnata_4 CTTTGCGGGCGGGCCCGAAAGTCAGTGGCGGTGCCGTCGGGCTTCAAGCG Ochrolechia_szatalaensis TAGTACAATC-TATCCCGCTTTGGAAGACC--GGGGGGGCTGGCCAGTCA Ochrolechia_upsaliensis TAGTACAA-CCTATCCCGCTTTGGAAGACCC-GGGGGGGCTGGCCAGTCA Ochrolechia_subviridis_1 TAGTACCTTTCTATCCCGCTTTGGAAGTCCC-GGGGGGGCTGGCCAGTCA Ochrolechia_subviridis_2 TAGTACATTTCTATCCCGCTTTGGAAGTCCT-GGGGGGGCTGGCCAGTCA Ochrolechia_subviridis_3 TAGTACATTTCTATCCCGCTTTGGAAGTCCC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_1 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_2 AAATTGTCTCGTA-CCCGCTTCAGAAGCCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_3 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_4 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_5 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_6 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_7 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTCGGGGGGGGCTGGCCAGTCA Ochrolechia_parella_8 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_9 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_10 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_11 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTCGGGGGGGGCTGGCCAGTCA Ochrolechia_parella_12 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_13 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_14 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_15 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGGGGGGCTGGCCAGTCA Ochrolechia_parella_16 AAATTGTCTCGTA-CCCGCTTCAGAAGTCTC-GGAGGGGCTGGCCAGTCA Ochrolechia_incarnata_1 AAATTGTCTCGTA-CCCGCTTGGGAAGTCCC-GGGGGGACTGGCCAGTCA Ochrolechia_incarnata_2 AAATTGTCTCGTA-CCCGCTTGGGAAGTCCC-GGGGGGACTGGCCAGTCA Ochrolechia_incarnata_3 AAATTGTCTCGTA-CCCGCTTTGGAAGTCCC-GGGGGGACTGGCCAGTCA Ochrolechia_incarnata_4 AAATTGTCTCGTA-CCCGCTTTGGAAGTCCC-GGGGGGACTGGCCAGTCA Ochrolechia_szatalaensis ACACCCGACATCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_upsaliensis ACACCCGACATCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_subviridis_1 ACACCCGACGTTTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_subviridis_2 ACACCCGACGTTTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_subviridis_3 ACACCCGACGTTTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_1 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_2 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_3 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_4 ACACCCGACGTCTCACGGTTGACCTCGGATCAG-TAGGGAT Ochrolechia_parella_5 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_6 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_7 ????????????????????????????????????????? Ochrolechia_parella_8 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_9 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_10 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_11 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_12 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_13 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_14 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_15 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_parella_16 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_incarnata_1 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_incarnata_2 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_incarnata_3 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT Ochrolechia_incarnata_4 ACACCCGACGTCTCACGGTTGACCTCGGATCAGGTAGGGAT ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = Ochrolechia_incarnata_Alignment) = unord: 1 - 541; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = Ochrolechia_incarnata_Alignment) = universal: 1 - 541; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = Ochrolechia_incarnata_Alignment) = 'Jukes-Cantor': 1 - 541; END; BEGIN TREES; Title 'Bayesian Tree from Ochrolechia incarnata ITS alignment"'; LINK Taxa = Taxa; TRANSLATE [0] 1 Ochrolechia_szatalaensis, [1] 2 Ochrolechia_upsaliensis, [2] 3 Ochrolechia_subviridis_1, [3] 4 Ochrolechia_subviridis_2, [4] 5 Ochrolechia_subviridis_3, [5] 6 Ochrolechia_parella_1, [6] 7 Ochrolechia_parella_2, [7] 8 Ochrolechia_parella_3, [8] 9 Ochrolechia_parella_4, [9] 10 Ochrolechia_parella_5, [10] 11 Ochrolechia_parella_6, [11] 12 Ochrolechia_parella_7, [12] 13 Ochrolechia_parella_8, [13] 14 Ochrolechia_parella_9, [14] 15 Ochrolechia_parella_10, [15] 16 Ochrolechia_parella_11, [16] 17 Ochrolechia_parella_12, [17] 18 Ochrolechia_parella_13, [18] 19 Ochrolechia_parella_14, [19] 20 Ochrolechia_parella_15, [20] 21 Ochrolechia_parella_16, [21] 22 Ochrolechia_incarnata_1, [22] 23 Ochrolechia_incarnata_2, [23] 24 Ochrolechia_incarnata_3, [24] 25 Ochrolechia_incarnata_4; TREE con_50_majrule = ((5:0.007212658,(3:0.00587599,4:0.002160599):0.002181006):0.00908236,((1:0.004629933,2:0.009845368):0.02314532,((24:0.0008590515,25:0.002113542,(22:0.0008615814,23:0.000880544):0.004597973):0.009688197,(21:0.001496399,(16:0.0009044566,17:0.002179155,18:0.0008965668,19:0.0009130421,20:0.0008987357,(6:0.0009135781,7:0.002198731,8:0.0009053135,9:0.0008999836,10:0.0008954698,11:0.0009267265,12:0.0009774601,13:0.0009128379,14:0.0009049311,15:0.0009083201):0.002171586):0.002144641):0.01604576):0.01313428):0.00908236)[% ] [% ] [% setBetweenBits = selected ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1528725090794; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2683530448223174069; tell It; setDefaultOrder 21 25 4 14 3 30 12 29 9 16 15 17 28 7 8 5 2 6 13 1 10 24 0 23 11; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2453632625394463824; mqVersion 304; checksumv 0 3 3533837418 null getNumChars 541 numChars 541 getNumTaxa 25 numTaxa 25 short true bits 15 states 15 sumSquaresStatesOnly 254083.0 sumSquares 254083.0 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 1328 592; setLocation 0 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #2683530448223174069 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 991.1528724862151.8054493591547985135; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1228 520; setLocation 0 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; setActive; 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 #2453632625394463824 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 215; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1228 520; setLocation 0 23; 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 on; toggleThinRows on; 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;