#NEXUS [written Sat Nov 05 22:56:01 GMT+08:00 2016 by Mesquite version 3.10 (build 765) at LS--20160307ROB/192.168.101.1] BEGIN TAXA; DIMENSIONS NTAX=24; TAXLABELS Microstoma_floccosum_Micro45 Cookeina_colensoi_C_col118 Cookeina_colensoi_C_col121 Cookeina_indica_C_ind119 Cookeina_korfii_CUP_SA_2454 Cookeina_korfii_strain_CUP_SA_1797 Cookeina_sinensis_C_sin111 Cookeina_sinensis_C_sin48 Cookeina_speciosa_C_spe6035 Cookeina_speciosa_C_spe31 Cookeina_sulcipes_2 Cookeina_sulcipes_1 Cookeina_venezuelae_C_ven43 Cookeina_venezuelae_C_ven42 Cookeina_insititia_C_ins126 Cookeina_insititia_C_ins125 'Cookeina garethjonesii_HK09' 'Cookeina garethjonesii_HK010' 'Cookeina tricholoma_MFLU 15-2359' 'Cookeina tricholoma_HK012' 'Cookeina indica_MFLU 16-0610' 'Cookeina sulcipes_MFLU 15-2358' Cookeina_cremeirosea_AS142 Cookeina_cremeirosea_AS210 ; END; BEGIN CHARACTERS; DIMENSIONS NCHAR=719; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Microstoma_floccosum_Micro45 ----------------------TTCCGTTAGGTGAACCTGCGGAA-GGATCATTAAAAACGTGCGG-CATTGAGGCGTCC----------------CTCGGGGCGCCTGTCGCCA-CG--CTGTGATGAAACACCTCCGTGTAC----ACTTACTTC-TGTTGCTTT-CCCGCCCTTCTC---CCGGGCGGGGAGAGCCAACT-TCAAAGCTCGT---TATCA----TATTGT-GGTCA--------GCATGAGC-GGCATTGTCCGCCTT---AAATATA---AAAGTTAAAACTTTCAACAACGGATCT-TTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGTATT-CCGGGGGGCATGCCTGTTCGAGCGTCGTCAAA-CACCCCTTCG--AGGCGTCTTCTGCTGAAGTCG--TCGTCGGTTATGGC-GGAGAA------TGTGCCGTTGTGGCACTCTCCCGCCCAAAGCCATCTGGCGGAGAGCCCTGGTCTGGCGCCGGCGTAGTAGGT----TTCTCGTTAAACACTCGTCGGAGCCAGGTTATCCAGCCGCGTCAAG---AACACT-TTCCAT--GTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCAATA------------- Cookeina_colensoi_C_col118 -------------------------CCGTAGGTGAACCTGCGGAA-GGATCATTAA-CAAGCGC-------------------------TCCGGCGCTCGGGCTCC--GGCCCCA-----CTTTTTCCACACACCTCCGTGTA-----TATGACCCAGTGTTGCTTC-CCGCCGCGCCTG---CCGGCCGGCGGGGAGATCCA-CCCAAACTCCA---CTTTG----TACTGTCTGTCA--------GTCTGAGC-GGCTCAGTCCGCG-----AATCAAAAACAAGTTAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAAC-ATCCTCCCC---CAGCGGCTT-TGCTGCCGTCT-TTGGGGGGTCATGGC-GGTGGA------GTGGCCTTGCGGCCGTCTCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTTGCCGTGGACGTAGTGAAA----AACCTCTCGACCGCTTGGCGCC-CCCAGTTATCCTGCCGCGAACAT---AGTTTT-TCAACGATATGGACCTCGGATCAGGTAGGGATACCCG----------------------------------- Cookeina_colensoi_C_col121 ------------------------TCCGTAGGTGAACCTGCGGAA-GGATCATTAA-CAAGCGC-------------------------TCCGGCGCTCGGGCTCC--GGCCCCA-----CCTTTTCCACACACCTCCGTGTA-----TATAACCCAGTGTTGCTTC-CCGCCGCGCCTG---CCGGCCGGCGGGGAGATCCA-CGCAAACTCCA---CTTTA----TACTGTCTGTCA--------GTCTGAGC-GGCTCAGTCCGCG-----AACCAAAAACAAGTTAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAAC-ATCCTCCCC---CAGCGGCTT-TGCTGCCGTCT-TTGGGGGGTCATGGC-GGTGGA------GTGGCCTCGCGGCCGTCTCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTTGCCGTGGACGTAGTGAAA----AACCTTTCGTCCGCCTGGCGCG-CCCAGTTATCCTGCCGCGAACGT---AGTTTT-TCAACGATATGGACCTCGGATCAGGTAGGGATACCC------------------------------------ Cookeina_indica_C_ind119 ----------------------TTTCCGTAGGTGAACCTGCGGAA-GGATCATTAA-AAGGCCCCT-----------------------TCGTGCGCTCGGGCTTC--GG-CCCG-TT--CTTTTTTCAAACACCTCTGTGTAC----CTTTACTATGTGTTGCTTC-CCGTCGCGCTTC-----GGCCGGCGGGAAGGCCCACCTTAAAACTCT---TTTAA--TTTTTTGTCAGTCA--------GTCTGAGCGGCATCAGTCCGCA-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCTCCT--CAGCGGTTT-TGC-GCCGTCT--GGGGGGGTCATGGT-GGAGGA---------------GCGCTTGCTCCCCGCTAAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAGTGAGA----TA-TTCTCGTCCGGTTGGTGCT-CCCGGTTATCCTGCCGTTGAAGCTTGCTA--T-TTATCT--ATTGACCTCGGATCAGGTAGGGATACCC------------------------------------ Cookeina_korfii_CUP_SA_2454 ----------------------CTTCCGTAGGTGAACCTGCGGAA-GGATCATTAACGAGGCGCCC-----------------------CCGCGCGCTCGGGCCCCCGGG-CCCGTTC--ACCTCACCAAACACCCCCGCGTAC----TACTACCTTCTGTTGCTTC-CCGCCGCTCCC------GGGCGGCGGGGAGGTCCG-CTCAAACCCCT---CTTTG----TG-AACTACCAGCTCA----GCCGCGTCGGGCGCAGCCCGCGCGAA-ATCTAAA---CAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAACTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCTCCCCGCCGCGGCGT-TGC-GCCGCGGGCGGGGGGGTCCTGGC-GGAGGA-----GCGGCCGGTCCGGCCGGCTCCCCGCCCAAAGCCATCTGGCGGAGCGCCCGTGGCGGCCCAGGACGTAGTGAGA----TG-CTCCCGTCCGTCGGCCACG-CCCGGCGCCCCCGCCGCGAACATC-CAGACTT-CTCGCC--ATTGACCTCGGATCAGGTAGGGATACCC------------------------------------ Cookeina_korfii_strain_CUP_SA_1797 ----------------------CTTCCGTAGGTGAACCTGCGGAA-GGATCATTAACGAGGCGCCC-----------------------CCGCGCGCTCGGGCCCCCGGG-CCCG-TC--ACCTCACCAAACACCCCGGCGTAC----CAATACCTTCCGTTGCTTC-CCGCCGCCCCCCC--GGGGGCGGCGGGGAGGTCCG-CTCAAACCCCT---CTTTG----TG-AATCGTCAGGTCA----GCCGCGCCGGGCGCAGCCCGCGCGGA-ATGAGAA---CAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAACTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCCCCCCACCGCGGCGT-TGC-GCCGCGGGCGGGGGGGTCCTGGC-GGAGGA-----GCGGCCGGTCCGGCCGGCTCCCCACCCAAAGCAATCTGGCGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------ Cookeina_sinensis_C_sin111 ---------------------------GTAGGTGAACCTGCGGAA-GGATCATTAACAAGGCGCCC-----------------------CCGTGCGCTCGGGCCTC--GG-CCCG-CC--ACCTCCTCAAACACCTCTGCGTAC----TCTTACCTT-TGTTGCTTC-CCGCCGCGCCCTC--GGGCGGGGCGGGGAGGTCCG-CTCAAACTCCT---TTCTG----TATTGCCAGTAGCTCA----GTCGTGCC-GGCTCAGTCCGCGCAAA-ACCTTAA---CCAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGTAACCCCCTCCCCC--CCGCGGCTT-TGC-GCCGCGG--CGGGGGGTCATGGC-GGAGGA----GGCGGCAGGTCCGCCGGCCTCCCCGCTCAAAGGAATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAGTGAGA----CG-CTCTCGTCCGTCGGCCCCG-CCCGGGCCTCCCGCCGCGACACCC-CAGACTT-CTCGCG--ATTGACCTCGGATCAGGTAGGGATACCCGCTG-------------------------------- Cookeina_sinensis_C_sin48 -------------------------------GTGAACCTGCGGAA-GGATCATTAACAAGGCGCCC-----------------------CCGTGCGCTCGGGCCTC--GG-CCCG-CC--ACCTCCTCAAACACCT-TGCGTAC----TCTTACCTT-TGTTGCTTC-CCGCCGCGCCCT---GGGCGGGGCGGGGAGGTCCG-CTCAAACTCCT---TTCTG----TATTGCCAGTAGCTCA----GTCGTGCC-GGCTCAGTCCGCGCAAA-ACCTTAA---CCAGTCAAAACTTTCAACAACGGAT-TTTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGTAA-CCCCTCCCCC--CCGCGGCTT-TGC-GCCGCGG--CGGGGGGTCATGGC-GGAGGA----GGCGGCAGGTCCGCCGGCCTCCCCGCTCAAAGGAATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAGTGAGA----CG-CTCTCGT-CGTCGGCCCCG-CCCGGGCCT-CCGCCGCCACACCC-CAGACTTACTCGCG--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAA------------------------------ Cookeina_speciosa_C_spe6035 --------------------------------------------A-GGATCATTAA-CAG-----CGCGCGGGAGGG-C----------CCGCGG-CTCCGGCCCG--GC-CCTC-CC--TCCTCTCCAAACACCTCCGTGTACGCTTTTCTACCCGGCGTTGCTTCCCCGCCGTGCCTTGCCGCCGGCGGGGGAGGGCCTCA-TGGAAACTCTTTTATTTTTTTGTATCTGTCATCTGCTCAGTCACGGGCGGC-GGCTCCGGCCGTGTCAG-CCGAGAA---ACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCCCC---CGGCGGCTT-CGCGGCCGC-C--CGGGGGGTCTTGGC-GGAGGAGCGCGCGCCCGACGGGCGCCGTCTCCCCGCTCAAAGCCATCTGGCGGAGAGTCTGTGGTCGCCGTGGACGTCGTGAGCATTCCAATCATCGTCCTGGCGGCGCGCCCCGGTTATCCAGCCGTA--------------------------------------------------------------------------------------- Cookeina_speciosa_C_spe31 ---------------------------GTTGGTGAACCTGCGGAA-GGATCATTAA-CAAGGGCGCGCGCGGGAGGG-C----------CCGCGG-CTCCGGCCCG--GC-CCTC-CC--TCCTCTCCACACCCCTCCGTGTACGCTTTTCTACCCGGCGTTGCTTCCCCGCCGTGCCTTGCCGCCGGCGGGGGAGGACCTCA-TGAAAATTC-----TTTTTTTGTTTCCGTCATCTGTTCAGTCATGGGCGGC-GGCTCCGTCCGCGTCGGCCCGAGAA---ACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCCCC---CGGCGGCTT-TGCGGCCGC-C--CGGGGGGTCTTGGC-GGAGGAGCGGGCGCCCGACGGGCGCCGCCTCCCCGCTCAAAGCCATCTGGCGGAGAGTCTGGGGTCGCCGTGGACGTCGTGAG-----CAATCATCGTCCCGGCGGCGCGCCCCGGTTATCCAGCCGTCGACAG--TGTTTTT-CTTCCG--ATTGACCTCGGATCAGGTAGGGACACCCGCTGAACTTAAGC-TA-TCAATAA------------ Cookeina_sulcipes_2 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAATATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAC-CCCCTCCCC---CGCCGGCTT-TGCGGCCGCGC--CGGGGGGTGTTGGCAGGAGGA--GCGTGCCCGTCGGGCGCCGCCTCCCCGCCCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCC?T?GACGTCTTGAACATTCCAATCATCGTCCGGGCGGTGCGCCGCGGCAGTCCAGCCGTTGACCAG-TGTTTTT-CTCGCG--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCAATAAGCCGGGAGGAA- Cookeina_sulcipes_1 ------------------------------------------------------------------------------------------------------------GT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAATTCAGAATTCAGCGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAC-CCCCTCCCC---CGCCGGCTT-TGCGGCCGCGC--CGGGGGGTGTTGGCAGGAGGA--GCGTGCCCGTCGGGCGCCGCCTCCCCGCCCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCC?TGGACGTCGTGAACATTCCAATCATCGTCCGGGCGGTGCGCCGCGGCAGTCCAGCCGTTGACCAG-TGTTTTT-CTCGCG--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCAATAG-CCGGGAGGAA- Cookeina_venezuelae_C_ven43 GGAGTAAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTAG-CAAGCGC-------------------------CCCGGCGCTCGGGCTCC--GG-CCCA-----TCAATCCCAAACACCCCCGCGTA-----TATGACCCAGTGTTGCTTC-CCGCCGCGCCTG---TCGGCCGGCGGGGAGATCCCCCGCAAACTCCA---TTTTG----TACTGTCTGTCA--------GTGTGAGC-GGCTCAGTCCGCG------ATCGAA---AAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTTCTGCCGGAGGGCATGCCTGTCCGAGCGTCGTGAAC-ACCCTCCCC---CAGCGGCCC-TGC-GCCGTCC-TCGGGGGGTCATGGC-GGTGGAGGGCCGGTCTCCCTGGGACCGCCTCCCCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGTGGACGTAGTGAAA----CACCCCTCGTCCCGTTGGCGCA-CCCAGTTATCCTGCCGCGAACAC---ACCTTT-CCAACG--ATTGACCTCGGATCAGGTAGGGATACGC----AACTTAAGCATA-TCAATAAGCCCGGGA---- Cookeina_venezuelae_C_ven42 ---ATAAAAAGTCGTAACAGGGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTAG-CAAGCGC-------------------------CCCGGCGCTCGGGCTCC--GG-CCCA-----TCAATCCCAAACACCCCCGCGTA-----TATGACCCAGTGTTGCTTC-CCGCCGCGCCTG---TCGGCCGGCGGGGAGATCCCCCGCAAACTCCA---TTTTG----TACTGTCTGTCA--------GTGTGAGC-GGCTCAGTCCGCG------ATCGAA---AAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTTCTGCCGGAGGGCATGCCTGTCCGAGCGTCGTGAAC-ACCCTCCCC---CAGCGGCCC-TGC-GCCGTCC-TCGGGGGGTCATGGC-GGTGGAGGGCCGGTCTCCCTGGGACCGCCTCCCCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGTGGACGTAGTGAAA----CACCCCTCGTCCCGTTGGCGCA-CCCAGTTATCCTGCCGCGAACAC---ACCTTT-CCAACG--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATTCAATAAGCCGAGGA---- Cookeina_insititia_C_ins126 -------------------------CCGTAGGTGAACCTGCGGAA-GGATCATTAA-AAGGCGCT------------------------TCCGGCGCTCGGGCTCC--GG-CCCA----TTCTCTTCTAAACACCTCTGCGTAC----TCTTACCTTGTGTTGCTTT-CCGCCACGCTTC-----GGCTGGCGGGAAGGGCCA-CGCAAACTCAA---TTTTA---TTTCTGTCAGTCA--------GTATGGC--GGCTCTGTCCGCG-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGCATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCGCC---CGGCGGCTT-CGC-GCCGCAC--CGGGCGGTCATGGC-GGAGGA-----AACGGGCCAAGGCTCGTCTCCCCGCCCAAAGATATCTGGCGGAGAGCCCGTGGTCGCCGTGGACGTAGTGAGA----CA-TTCTCGTCCGTTTGGCGTG-CCCGGTTATCCTGCCGCGACGTTT--CAATCT-CGACCT--ATTGACCTCGGATCAGGTAGGGATACCC------------------------------------ Cookeina_insititia_C_ins125 --------------------GGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTAA-AAGGCGCT------------------------TCCGGCGCTCGGGCTCC--GG-CCCA----TTCTCTTCTAAACACCTCTGCGTAC----TCTTACCTTGTGTTGCTTT-CCGCCACGCTTC-----GGCTGGCGGGAAGGGCCA-CGCAAACTCAA---TTTTA---TTTCTGTCAGTCA--------GTATGGC--GGCTCTGTCCGCG-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGCATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCGCC---CGGCGGCTT-CGC-GCCGCAC--CGGGCGGTCATGGC-GGAGGA-----AACGGGCCAAGGCTCGTCTCCCCGCCCAAAGATATCTGGCGGAGAGCCCGTGGTCGCCGTGGACGTAGTGAGA----CA-TTCTCGTCCGTTTGGCGTG-CCCGGTTATCCTGCCGCGACGTTT--CAATCT-CGACCT--ATTGACCTCGGATCAGGTAGGGA----------------------------------------- 'Cookeina garethjonesii_HK09' --------------------------------------ACTGCGG-AGGACATTAA-CAGGCGCCCGCGCGGGGAGGTC----------CCGCGGCCCCGGCCCGG--GC-CTCC-CC--CCCCTTCCCCAACCCTCCGTGTACTCTTTTCTACCCGGCGTTGCTTCCCCGCCGTGCCTAGCCGCCGGCGGGGGAGGGCCTCA-TGAAAACTCTT---TTTTATAGTTTCTGTCATTTGTTCAGCGGTGGGCGCC-GGCTCCGGCCGCGTCCGCCGACCAA---ACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCCCC---CGCCGGCTT-TGCGGCCGCGC--CGGGGGGTGTTGGC-GGAGGA--GCGCGCCCGACGGGCGCCGCCTCCCCGCTCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCCGTGGACGTCGTGAACATTCCAATCATCGTCCGACCGGTGCGCCGCGGCGGTCCAGCCGTTGACCTC-TGTTTTTTCTCGCG---ATGACCTC-GATCAGAGACGGACACCCGCTGAACTTAAGCATA-TCTAAAGGCCGGAGGAAAT 'Cookeina garethjonesii_HK010' --------------------------------------TACTCGG-AGGACATTAA-CAGGCGCCCGCGCGGGGAGGTC----------CCGCGG-CCCGGAGAAA--GA-TTCC-CC--CCCTTCCCTCAACCCTCCGTGTACTCTTTTCTACCCGGCGTTGCTTCCCCGCCGTGCCTAGCCGCCGGCGGGGGAGGGCCTCA-TGAAAACTCTT---TTTTATAGTTTCTGTCATTTGTTCAGCGGTGGGCGCC-GGCTCCGGCCGCGTCCGCCGACCAA---ACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA-CCCCTCCCC---CGCCGGCTT-TGCGGCCGCGC--CGGGGGGTGTTGGC-GGAGGA--GCGCGCCCGACGGGCGCCGCCTCCCCGCTCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCCGTGGACGTCGTGAACATTCCAATCATCGTCCGACCGGTGCGCCGCGGCGGTCCAGCCGTTGACCTC-TGTTTTTTCTCGCG--ATTGACCTCGGATCGGAGACCGACACCCGCTGAACTTAAGCATA-TCAAAAAGGGGGAAGGAAA 'Cookeina tricholoma_MFLU 15-2359' AAGGTAAAAAAAGGTAACAAGGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTACGAAGGCGCC------------------------TCGCGCGCTCGGGCTTC--GG-CCCG-CC--ACCTTTCCAAACACCTCTGCGTAC-----TTAACTTT-TGTTGCTTC-CCGCCGCGCCTC---GCGGCCGGCGGGGAGGTCCG-CTCAAACTCCT---TTTTG----TATTGGCAGTAGCTCA----GTCGCGCC-GGCTCAGTCCGCGCAAAGATATAAA---CAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCTCCC--CCGCGGTTT-TGC-GCCGCGG--CGGGAGGTCATGGC-GGAGGA-----GCGGCTGGTCTTGCCGCCTCCCCGCTCGAAGGCATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAGTGAGA----CA-CTCTCGTCCGTCGGCCCCG-TCCGGCCCTCCCGCCGCGACACCC-CAGACTT-CTCGCG--ATTGACCTCGGATCGGAGGTGGATACCCGCTGAACTTAAGCATA-TCATAAGGCCGGAGGAAAT 'Cookeina tricholoma_HK012' GAAGGAAAAAAGTGTAACAAGGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTACGAAGGCGCC------------------------TCGCGCGCTCGGGCTTC--GG-CCCG-CC--ACCTTTCCAAACACCTCTGCGTAC-----TTAACTTT-TGTTGCTTC-CCGCCGCGCCTC---GCGGCCGGCGGGGAGGTCCG-CTCAAACTCCT---TTTTG----TATTGGCAGTAGCTCA----GTCGCGCC-GGCTCAGTCCGCGCAAAGATATAAA---CAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCTCCC--CCGCGGTTT-TGC-GCCGCGG--CGGGAGGTCATGGC-GGAGGA-----GCGGCTGGTCTTGCCGCCTCCCCGCTCGAAGGCATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAGTGAGA----CA-CTCTCGTCCGTCGGCCCCG-TCCGGCCCTCCCGCCGCGACACCC-CAGACTT-CTCGCG--ATTGACCTCGGATCAGGTAGAACTACCCGCTGAACTTAAGCA-A-TCAAAAGGCGGGAAGAAA- 'Cookeina indica_MFLU 16-0610' AAGGTAAAAAAATGTAACAAGGTTTCCGTAGGTGAACCTGCGGAA-GGATCATTAA-AAGGCGCCT-----------------------TCGTGCGCTCGGGCTTC--GG-TCCG-TT--CTTTTTTCAAACACCTCTGTGTAC----CTTTACTATGTGTTGCTTC-CCGTCGCGCTTC-----GGCCGGCGGGAAGGCCCACCTTAAAACTCT---TTTAA--TTTTTTGTCAGTCA--------GTCTGAGCGGCATCAGTCCGCA-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA-CCCCTCTCCT--CAGCGGTTT-TGC-GCCGTCT--GGGGGGGTCATGGT-GGAGGA---------------GCGCTTGCTCCCCGCTAAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAGTGAGA----TA-TTCTCGTCCGGTTGGTGCT-CCCGGTTATCCTGCCGTTGAAGCTTGCTA--T-TTATCT--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCATAAGGCCGGAGGAAAC 'Cookeina sulcipes_MFLU 15-2358' GGAAGTAAAAGTCGTAACAAGGTTTCCGYAGGTGAACCTGCGGAA-GGATCATTAA-CAGGCGCCCGCGCGGGGGGGTC----------CCGCGG-CTCCGGCCCG--GC-CCTC-CC--TCCCTCTTCAAACCCTCCGTGTACTCTGTTCTACCCGGCGTTGCTTCCCCGCCGTGCCTAGCCGCCGGCGGGGGAGGGCTTCA-TGAAAACTCTT---TTTTAT-GTTTCTGTCATTTGTTCAGTGGTGGGCGCC-GGCTCCGGCCGCGCCCGCCGACCAA---ACTGTCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAC-CCCCTCCCC---CGCCGGCTT-TGCGGCCGCGC--CGGGGGGTGTTGGC-GGAGGA--GCGTGCCCGTCGGGCGCCGCCTCCCCGCCCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCCGTGGACGTCGTGAACATTCCAATCATCGTCCGGGCGGTGCGCCGCGGCAGTCCAGCCGTTGACCAG-TGTTTTT-CTCGCG--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCAATAA------------ Cookeina_cremeirosea_AS142 -----------------------TTCCGTAGGTGAACCTGCGGAA-GGATCATTAA-AAGGCGCCCTCGTGCGCTCGGGCTTCGGTCCGTCGTGCGCTCGGGCTTC--GG-TCCG-TTTATTTTTTTCAAACACCTCTGTGTAC----CTTTACCTTGTGTTGCTTC-CCGCCGCGCTTC-----GGCCGGCGGGAAGGCCTACCTTAAAACTCT---TTTTG---TTTATGTCAGTCA--------GTCTGAGCGGCATCAGTCCGCA-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAGAAG-CCCCTCTCCT--CAGCGGTTT-TGC-GCCGTCT--GGGGGGGTCATGGT-GGAGGA---------------GCGTTTGCTTCCCGCTTAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAGTGAGA----TA-TTCTCGTCCGGTTGGTGCT-CCCGGTTATCTAGCCGTTGAAGCTTTGCATTT-TTATCT--ATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA-TCAATAAGCGGAGGAA--- Cookeina_cremeirosea_AS210 ------------------------TCCGTAGGTGAACCTGCGGAAGGGATCATTAA-AAGGCGCCC-----------------------TCGTGCGCTCGGGCTTC--GG-TCCG-TTTATTTTTTTCAAACACCTCTGTGTAC----CTTTACTTTGTGTTGCTTC-CCGCCGCGCTTC-----GGCCGGCGGGAAGGCCTACCTTAAAACTCT---TTTTG---TTTATGTCAGTCA--------GTCTGAGCGGCATCAGTCCGCA-----AATCAAA---CAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAGAAG-CCCCTCTCCT--CAGCGGTTT-TGC-GCCGTCT--GGGGGGGTCATGGT-GGAGGA---------------GCGTTTGCTTCCCGCTTAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAGTGAGA----TA-TTCTCGTCCGGTTGGTGCT-CCCGGTTATCTAGCCGTTGAAGCTTTGCATTT-TTATCT--ATTGACCTCGGATCAGGTAGGGATACT------------------------------------- ; END; begin paup; outgroup Microstoma_floccosum_Micro45; set maxtrees = 1000 increase = no; set criterion = parsimony; hsearch addseq = random nreps = 1000; roottrees outroot = monophyl; pscores All / ci = yes tl = yes hi = yes rc = yes ri = yes khtest = yes; savetrees file = gibbphytest_mp.tre brlens = yes; bootstrap nreps = 1000 Keepall = yes / AddSeq = random nreps = 10; savetrees file = gibbpnytest.tre from = 1 to = 1 savebootp = both maxdec = 0; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 719; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 719; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 719; END; BEGIN TREES; Title 'Trees from "gibbphytest_mp.tre"'; ID 015834f4aa511; LINK Taxa = Taxa; TRANSLATE [0] 1 Microstoma_floccosum_Micro45, [1] 2 Cookeina_colensoi_C_col118, [2] 3 Cookeina_colensoi_C_col121, [3] 4 Cookeina_indica_C_ind119, [4] 5 Cookeina_korfii_CUP_SA_2454, [5] 6 Cookeina_korfii_strain_CUP_SA_1797, [6] 7 Cookeina_sinensis_C_sin111, [7] 8 Cookeina_sinensis_C_sin48, [8] 9 Cookeina_speciosa_C_spe6035, [9] 10 Cookeina_speciosa_C_spe31, [10] 11 Cookeina_sulcipes_2, [11] 12 Cookeina_sulcipes_1, [12] 13 Cookeina_venezuelae_C_ven43, [13] 14 Cookeina_venezuelae_C_ven42, [14] 15 Cookeina_insititia_C_ins126, [15] 16 Cookeina_insititia_C_ins125, [16] 17 'Cookeina garethjonesii_HK09', [17] 18 'Cookeina garethjonesii_HK010', [18] 19 'Cookeina tricholoma_MFLU 15-2359', [19] 20 'Cookeina tricholoma_HK012', [20] 21 'Cookeina indica_MFLU 16-0610', [21] 22 'Cookeina sulcipes_MFLU 15-2358', [22] 23 Cookeina_cremeirosea_AS142, [23] 24 Cookeina_cremeirosea_AS210; TREE PAUP_1 = (1:66,((((((2:4,3:7):19,(13:3,14:2):23):24,(15:0.0,16:0.0):41):23,((9:9,10:10):16,(((11:5,22:0.0):0.0,12:6):12,(17:11,18:13):25):21):63):34,(((5:7,6:12):38,(7:0.0,8:2):17):12,(19:9,20:7):13):34):28,((4:2,21:0.0):11,(23:1,24:1):14):43):62):0.0; TREE PAUP_2 = (1:66,((((((2:4,3:7):19,(13:3,14:2):23):24,(15:0.0,16:0.0):41):23,((9:9,10:10):16,(((11:5,12:1):5,22:0.0):12,(17:11,18:13):25):21):63):34,(((5:7,6:12):38,(7:0.0,8:2):17):12,(19:9,20:7):13):34):28,((4:2,21:0.0):11,(23:1,24:1):14):43):62):0.0; TREE PAUP_3 = (1:66,((((((2:4,3:7):19,(13:3,14:2):23):24,(15:0.0,16:0.0):41):23,((9:9,10:10):16,((11:5,(12:6,22:0.0):0.0):12,(17:11,18:13):25):21):63):34,(((5:7,6:12):38,(7:0.0,8:2):17):12,(19:9,20:7):13):34):28,((4:2,21:0.0):11,(23:1,24:1):14):43):62):0.0; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1478357761977; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5106024598121966881; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2595737344492326244; mqVersion 310; checksumv 0 3 1047438559 null getNumChars 719 numChars 719 getNumTaxa 24 numTaxa 24 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 273440.0 sumSquares -9.2233720368547707E18 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 195; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 872 464; setLocation 326 42; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5106024598121966881 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 015834f4aa511; toggleUseWeights off; endTell; setAssignedID 1119.1478357203353.6988268996870699516; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 677 392; setLocation 326 42; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 off; 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; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2595737344492326244 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 677 392; setLocation 326 42; 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.AlterData.AlterData; tell It; toggleBySubmenus off; 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;