#NEXUS [written Tue Dec 15 11:22:35 MST 2015 by Mesquite version 2.75 (build 564) at DPBIOL-gwx8dp1/129.123.16.194] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=20; TAXLABELS Cookeina_tricholoma_AF394023 Cookeina_tricholoma_AF394025 Cookeina_sinensis_AF394028 Cookeina_sinensis_AF394027 Cookeina_colensoi_AF394532 Cookeina_colensoi_AF394531 Cookeina_colensoi_AF394040 Cookeina_colensoi_AF394038 Cookeina_venezuelae_AF394041 Cookeina_venezuelae_AF394044 Cookeina_insititia_AF394032 Cookeina_insititia_AF394031 Cookeina_indica_AF394029 Cookeina_cremeirosea_AS142 Cookeina_cremeirosea_AS210 Cookeina_speciosa_AF394018 Cookeina_speciosa_AF394010 Cookeina_speciosa_AF394003 Microstoma_floccosum_AF394045 Microstoma_floccosum_AF394046 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=759; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = -; MATRIX Cookeina_tricholoma_AF394023 AAAAGTCGTAACAAGGTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTACGAAGGCGCCTCGC----GCGCTCGGGCTTC---GG---CCCGC------ Cookeina_tricholoma_AF394025 ---------------------GT-AGGTGAACCTGCGGAAGG-ATCATTACGAAGGCGCCTCGC----GCGCTCGGGCTTC---GG---CCCGC------ Cookeina_sinensis_AF394028 ---------------------GT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGGCGCCCCC---GTGCGCTCGGGCCTC---GG---CCCGC------ Cookeina_sinensis_AF394027 --------------------------GTGAACCTGCGGAAGG-ATCATTAACAAGGCGCCCCC---GTGCGCTCGGGCCTC---GG---CCCGC------ Cookeina_colensoi_AF394532 -------------------CCGT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGCGC---TCC---GGCGCTCGGGC-TCC--GG---CCC-------- Cookeina_colensoi_AF394531 ------------------TCCGT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGCGC---TCC---GGCGCTCGGGC-TCC--GG---CCC-------- Cookeina_colensoi_AF394040 ------------------TCCGT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGCGC---TCC---GGCGCTCGGGC-TCC--GG---CCC-------- Cookeina_colensoi_AF394038 ---------------------GT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGCGC---TCC---GGCGCTCGGGC-TCC--GG---CCC-------- Cookeina_venezuelae_AF394041 AAAAGTCGTAACAAGGTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAACAAGCGCC--TCC---GGCGCTCGGGCTTC---GG---CC--------- Cookeina_venezuelae_AF394044 AAAAGTCGTAACAAGGTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAGCAAGCGCC---CC---GGCGCTCGGGC-TCC--GG---CC--------- Cookeina_insititia_AF394032 --------------GGTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAAAA-GGCGC-TTCC---GGCGCTCGGGC-TCC--GG---CC--------- Cookeina_insititia_AF394031 ---------------GTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAAAA-GGCGC-TTC---TGGCGCTCGGGC-TCC--GG---CC--------- Cookeina_indica_AF394029 ----------------TTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAAAA-GGCCCCTTC---GTGCGCTCGGGCTTC---GG---CCCG------- Cookeina_cremeirosea_AS142 -----------------TTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAAAA-GGCGCCCTC---GTGCGCTCGGGCTTC---GG--TCCGTCGTGCGC Cookeina_cremeirosea_AS210 ------------------TCCGT-AGGTGAACCTGCGGAAGGGATCATTAAAA-GGCGCCCTC---GTGCGCTCGGGCTTC---GG--TCC-G------- Cookeina_speciosa_AF394018 ---------------------------------------AGG-ATCATTAACA-GGCGCCCCC----TGCGGCGCG-CGG--GAGGG--CCCGCGGCTCC Cookeina_speciosa_AF394010 ------------------------------ACTTTCGAAAG-ACTCATTAACA-GAGCGCTCCC---TGCGGCGCGCG-GG-GAGAG-TCCCGCGGCCCC Cookeina_speciosa_AF394003 ------------------------------------AGGAGG-ATTATTAACAAGGGGCGCCCCCCCGGGGGCGCGCGCGG-GAGGG-CCCCTCGCGGCC Microstoma_floccosum_AF394045 AAAAGTCGTAACAAGGTTTCCGT-AGGTGAACCTGCGGAAGG-ATCATTAAAAACGTGCATCTC--GTGG-AT-GGCATT--GAGGCGTCCCTCGGGGCG Microstoma_floccosum_AF394046 ----------------TTTCCGTTAGGTGAACCTGCGGAAGG-ATCATTAAAAACGTGCATCTC--GTGG-AT-GGCATT--GAGGCGTCCCTCGGGGCG Cookeina_tricholoma_AF394023 ----------------CA-CCTTT-CCAAACACCTCTGCGTA--CTT----AAC-TTTTGTTGCTT--CCCGCCGCGCC-T-CGCGGCCGGCGGGGAGGT Cookeina_tricholoma_AF394025 ----------------CA-CCTTT-CCAAACACCTCTGCGTA--CTT----AAC-TTTTGTTGCTT--CCCGCCGCGCC-T-CGCGGCCGGCGGGGAGGT Cookeina_sinensis_AF394028 ----------------CA-CCTCCT-CAAACACCTCTGCGTACTCTT----A-CC-TTTGTTGCTT--CCCGCCGCGCCCT-CGGGCGGGGCGGGGAGGT Cookeina_sinensis_AF394027 ----------------CA-CCTCCT-CAAACACCT-TGCGTACTCTT----A-CC-TTTGTTGCTT--CCCGCCGCGCCCT--GGGCGGGGCGGGGAGGT Cookeina_colensoi_AF394532 ----------------CA-CTTTTTCCACACACCTCCGTGTATATG-----A-CCCAGTGTTGCTT--CCCGCCGCGCC-T-GCCGGCCGGCGGGGAGAT Cookeina_colensoi_AF394531 ----------------CA-CCTTTTCCACACACCTCCGTGTATAT------AACCCAGTGTTGCTT--CCCGCCGCGCC-T-GCCGGCCGGCGGGGAGAT Cookeina_colensoi_AF394040 ----------------CA-CCTTTTCCACACACCTCCGTGTATATG-----A-CCCAGTGTTGCTT--CCCGCCGCGCC--GGCCGGCCGGCGGGGAGAT Cookeina_colensoi_AF394038 ----------------CA-CTTTTTCCACACACCTCCGTGTATATG-----A-CCCAGTGTTGCTT--CCCGCCGCGCC-T-GCCGGCCGGCGGGGAGAT Cookeina_venezuelae_AF394041 ----------------CA-TCGTTTTCAAACCCCTCTGTGTATATG-----A-CCCAGTGTTGCTTT--CCGTCGCGCC-TGT-CGGCCGGCGGGAAGGT Cookeina_venezuelae_AF394044 ----------------CA-TCAATCCCAAACACCCCCGCGTATATG-----A-CCCAGTGTTGCTT--CCCGCCGCGCC-TGT-CGGCCGGCGGGGAGAT Cookeina_insititia_AF394032 ----------------CATTCTCTTCTAAACACCTCTGCGTACTCTT----A-CCTTGTGTTGCTTT--CCGCCACGC--TT--CGGCTGGCGGGAAGGG Cookeina_insititia_AF394031 ----------------CATTCCCTTCTAAACACCTCTGCGTACTCTT----A-CCTTGTGTTGCTTT--CCGCCACGC--TT--CGGCTGGCGGGAAGGG Cookeina_indica_AF394029 -----------------TTCTTTTTTCAAACACCTCTGTGTAC-CTTT---A-CTATGTGTTGCTT--CCCGTCGCGC--TT--CGGCCGGCGGGAAGGC Cookeina_cremeirosea_AS142 TCGGGCTTCGGTCCGTTTATTTTTTTCAAACACCTCTGTGTAC-CTTT---A-CCTTGTGTTGCTT--CCCGCCGCGC--TT--CGGCCGGCGGGAAGG- Cookeina_cremeirosea_AS210 ---------------TTTATTTTTTTCAAACACCTCTGTGTAC-CTTT---A-CTTTGTGTTGCTT--CCCGCCGCGC--TT--CGGCCGGCGGGAAGG- Cookeina_speciosa_AF394018 GGCCCGGCCC-----TCCCTCCTCTCCAAACACCTCCGTGTACGCTTTTCTA-CCCGGCGTTGCTT-CCCCGCCGTGCC-TTGCCGCCGGCGGGGGAGGG Cookeina_speciosa_AF394010 GGCCCGGGCC----TCCCCCCCTCCTCAAAC-CCTCCGTGTACTCTTTTCTA-CCCGGCGTTGCTT-CCCCGCCGTGCC-TAGCCGCCGGCAGGGGAGGG Cookeina_speciosa_AF394003 C--------------TCCCTCCTCTCCAAACCCCTCCGTGTACGCTTAT--A-CCGGC-GTTGCTT-CCCCGCCGTGCC-TTGCCGCCGGCGGGGGAGGA Microstoma_floccosum_AF394045 CCTGTCGCCACG-------CTGTGATGAAACACCTCCGTGTACACTT----A-CTT-CTGTTGCTTT-CCCGCCCTTC--T----CCCGGGCGGGGAGAG Microstoma_floccosum_AF394046 CCTGTCGCCACG-------CTGTGATGAAACACCTCCGTGTACACTT----A-CTT-CTGTTGCTTT-CCCGCCCTTC--T----CCCGGGCGGGGAGAG Cookeina_tricholoma_AF394023 CCGC--T--C--AAA--CTCCTTTTTTGTATT----GGCA--GT-AG-CTCAGT-GC-GCCGGC-TCAG--------TCCGCGCAAAGATATAAACAAGT Cookeina_tricholoma_AF394025 CCGC--T--C--AAA--CTCCTTTTT-GTATT----GGCA--GT-AG-CTCAGTCGC-GCCGGC-TCAG--------TCCGCGCAAAGATATAAACAAGT Cookeina_sinensis_AF394028 CCGC--T--C--AAA--CTCCTTTCT-GTATT----GCCA--GT-AG-CTCAGTCGT-GCCGGC-TCAG--------TCCGCGCAAAACCTTAACC-AGT Cookeina_sinensis_AF394027 CCGC--T--C--AAA--CTCCTTTCT-GTATT----GCCA--GT-AG-CTCAGTCGT-GCCGGC-TCAG--------TCCGCGCAAAACCTTAACC-AGT Cookeina_colensoi_AF394532 CC---A-CCC--AAA--CTCCACTTT-GTA------CTGTCTGTCAGTCTGA-------GCGGC-TCAG--------TCCGCG---AATCAAAAACAAGT Cookeina_colensoi_AF394531 CC---A-CGC--AAA--CTCCACTTT-ATA------CTGTCTGTCAGTCTGA-------GCGGC-TCAG--------TCCGCG---AACCAAAAACAAGT Cookeina_colensoi_AF394040 CC---A-CGC--AAA--CTCCACTTT-GTA------CTGTCTGTCAGTCTGA-------GCGGC-TCAG--------TCCGCG-----AATCAAAAA-CT Cookeina_colensoi_AF394038 CC---A-CGC--AAA--CTCCACTTT-GTA------CTGTCTGTCAGTCTGA-------GCGGC-TCAG--------TCCGCG-----AATCAAAAA-GT Cookeina_venezuelae_AF394041 CCC--AT-GC--AAA--CTCCATTTT-GTT------CTGCCTGTCAGTCTGA-------GCGGC-TCAG--------TCCGC----AATTTCAATAA-GT Cookeina_venezuelae_AF394044 CCCCC---GC--AAA--CTCCATTTT-GTA------CTGTCTGTCAGTGTGA-------GCGGC-TCAG--------TCCGCG------ATCGAAAAAGT Cookeina_insititia_AF394032 CC---A-CGC--AAA--CTCAATTTT-ATTT-----CTGTCAGTCAGTATG--------GCGGC-TCTG--------TCCGCG-----AATCAAA---CA Cookeina_insititia_AF394031 CC----TCGC--AAA--CTCGATTTT-ATTT-----CTGTCAGTCAGTATG--------GCGGC-TCTG--------TCCGCG-----AATCAAACAAGT Cookeina_indica_AF394029 CC-----ACCTTAAAA-CTCTTTTAATTTTT------TGTCAGTCAGTCTGA-------GCGGCATCAG--------TCCGC-----AAATCAAACAAGT Cookeina_cremeirosea_AS142 CC----TACCTTAAAA-CTCTTTTTGTTTA-------TGTCAGTCAGTCTGA-------GCGGCATCAG--------TCCGC-----AAATCAAACAAGT Cookeina_cremeirosea_AS210 CC----TACCTTAAAA-CTCTTTTTGTTTA-------TGTCAGTCAGTCTGA-------GCGGCATCAG--------TCCGC-----AAATCAAACAAGT Cookeina_speciosa_AF394018 CC----T-CATGGAAA-CTCTTTTATTTTTTTGTATCTGTCA-TCTG-CTCAGTCACGGGCGGCGGCTCCGGCCGTGTCAGCC----GA--GAAAC-TGT Cookeina_speciosa_AF394010 CCTC-AT--G--AAAA-CTCTTTTTTATAGTTT---CTGTCATTT-GT-TCAGCGGTGGGCGCCGGCTCCGGCCGCGTCCGCC----GA-CCAAAC-TGT Cookeina_speciosa_AF394003 CC----T-CATGAAAA-TTCTTTTTTT--GTTT---CCGTCA-TCTGATTC----GTGGGCGGCGGCTCCGTCCGCGTCGGCCC---GA--GAAAC-TGT Microstoma_floccosum_AF394045 CC----AAC-TTCAAAGCTCGTTATCATAT-------TGT-GGTCAG---CA-------------TGAGCGGCATTGTCCGCC---TTAAATATAAAAGT Microstoma_floccosum_AF394046 CC----AAC-TTCAAAGCTCGTTATCATAT-------TGT-GGTCAG---CA-------------TGAGCGGCATTGTCCGCC---TTAAATATAAAAGT Cookeina_tricholoma_AF394023 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_tricholoma_AF394025 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_sinensis_AF394028 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_sinensis_AF394027 CAAAA-CTTTCAACAACGGA-TTTTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_colensoi_AF394532 TAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_colensoi_AF394531 TAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_colensoi_AF394040 TAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_colensoi_AF394038 TAAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_venezuelae_AF394041 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGATTTCAGTGAATCATCGAA Cookeina_venezuelae_AF394044 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_insititia_AF394032 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_insititia_AF394031 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_indica_AF394029 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_cremeirosea_AS142 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_cremeirosea_AS210 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_speciosa_AF394018 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_speciosa_AF394010 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_speciosa_AF394003 CAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Microstoma_floccosum_AF394045 TAAAA-CTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Microstoma_floccosum_AF394046 TAAAA-CTTTCAACAACGGATCT-TTGGTTCCCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA Cookeina_tricholoma_AF394023 TCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA--CCCCT-CTCCCCC--GCGGTTTTGC-GCCGCGGC Cookeina_tricholoma_AF394025 TCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA--CCCCT-CTCCCCC--GCGGTTTTGC-GCCGCGGC Cookeina_sinensis_AF394028 TCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGTAA--CCCCC--TCCCCCCCGCGGCTTTGC-GCCGCGGC Cookeina_sinensis_AF394027 TCTTTGAACGCACATTGCGCCCTCCGGCATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGTAA---CCCC--TCCCCCCCGCGGCTTTGC-GCCGCGGC Cookeina_colensoi_AF394532 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAACA-----TCCTCCCCC-AGCGGCTTTGCTGCCGTCTT Cookeina_colensoi_AF394531 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAACA-----TCCTCCCCC-AGCGGCTTTGCTGCCGTCTT Cookeina_colensoi_AF394040 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGTGAACA-----TCCTCCCCC-AGCGGCTTTGCTGTCGTCTT Cookeina_colensoi_AF394038 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAACA-----TCCTCCCCC-AGCGGCTTTGCTGCCGTCTT Cookeina_venezuelae_AF394041 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGTGAACA--CCCT---CCCCC-AGCGGCCTTGC-GGGGTCGT Cookeina_venezuelae_AF394044 TCTTTGAACGCACATTGCGCCCTCTGGTTCTGCCGGAGGGCATGCCTGTCCGAGCGTCGTGAACA--CCCT---CCCCC-AGCGGCCCTGC-GCCGTCCT Cookeina_insititia_AF394032 TCTTTGAACGCACATTGCGCCCTCTGGCATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAAAAA--CCCCT---CGCCC-GGCGGCTTCGC-GCCGCACC Cookeina_insititia_AF394031 TCTTTGAACGCACATTGCGCCCTCTGGCATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAGAAA--CCCCT---CGCCC-AGCGGCTTCGC-GCCGCGT- Cookeina_indica_AF394029 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAGAAA--CCCCTC-TCCTC--AGCGGTTTTGC-GCCGTCT- Cookeina_cremeirosea_AS142 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAGAAG--CCCCTC-T--CCTCAGCGGTTTTGC-GCCGTCT- Cookeina_cremeirosea_AS210 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGAGGGCATGCCTGTCCGAGCGTCGAGAAG--CCCCTC-T--CCTCAGCGGTTTTGC-GCCGTCT- Cookeina_speciosa_AF394018 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA--CCCCT----CCCCCGGCGGCTTCGCGGCCGCCCG Cookeina_speciosa_AF394010 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA--CCCCT----CCCCCGCCGGCTTTGC-GGCCGCGC Cookeina_speciosa_AF394003 TCTTTGAACGCACATTGCGCCCTCTGGTATT-CCGGGGGGCATGCCTGTCCGAGCGTCGAAAAA--CCCCT----CCCCCGGCGGCTTTGC-GGCCGCCC Microstoma_floccosum_AF394045 TCTTTGAACGCACATTGCGCCCTCCGGTATT-CCGGGGGGCATGCCTGTTCGAGCGTCGTCAAACACCCCTT------CGAGGCG-TCTTCTGCTGAAGT Microstoma_floccosum_AF394046 TCTTTGAACGCACATTGCGCCCTCCGGTATT-CCGGGGGGCATGCCTGTTCGAGCGTCGTCAAACACCCCTT------CGAGGCG-TCTTCTGCTGAAGT Cookeina_tricholoma_AF394023 ----GGGAGGTCATGGCGGAGGA--GCGGCTGGTCTT----GCCG-CC--TCCCCGCTCGAAGGCATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAG Cookeina_tricholoma_AF394025 ----GGGAGGTCATGGCGGAGGA--GCGGCTGGTCTT----GCCG-CC--TCCCCGCTCGAAGGCATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAG Cookeina_sinensis_AF394028 ----GGGGGGTCATGGCGGAGGA-GGCGGCAGGTCC-----GCCGGCC--TCCCCGCTCAAAGGAATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAG Cookeina_sinensis_AF394027 ----GGGGGGTCATGGCGGAGGA-GGCGGCAGGTCC-----GCCGGCC--TCCCCGCTCAAAGGAATCTGGCGGAGAGCCCGTGGCGGCCGTGGACGTAG Cookeina_colensoi_AF394532 T---GGGGGGTCATGGCGGTGGA--GTGGCC--TTGC---GGCCG-TC--TCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTTGCCGTGGACGTAG Cookeina_colensoi_AF394531 T---GGGGGGTCATGGCGGTGGA--GTGGCC--TCGC---GGCCG-TC--TCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTTGCCGTGGACGTAG Cookeina_colensoi_AF394040 T---GGGGGGTCATGGCGGTGGAA-GTGGCC--TCGC---GGCCG-TC--TCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGCGGACGTAG Cookeina_colensoi_AF394038 T---GGGGGGTCATGGCGGTGGA--GTGGCC--TCGC---GGCCG-TC--TCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGCGGACGTAG Cookeina_venezuelae_AF394041 CCTTGGGGGGTCATGGCGGTGGA--GGGGGTC-TCCC--TGGGACCGC-TTCCTCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGTGGACGTAG Cookeina_venezuelae_AF394044 C---GGGGGGTCATGGCGGTGGA---GGGCCGGTCTCCCTGGGACCGCC-TCCCCGCCCAAAGGCATCTGGCGGAGAGCCTGTGGTCGCCGTGGACGTAG Cookeina_insititia_AF394032 ----GGGCGGTCATGGCGGAGGAAA-CGGGCCAA------GGCTCGTC--TCCCCGCCCAAAGATATCTGGCGGAGAGCCCGTGGTCGCCGTGGACGTAG Cookeina_insititia_AF394031 ---GGGGCGGTCATGGCGGAGGAA-GCGGGCCAA------GGCTCGTC--TCCCCGCCCAAAGATATCTGGCGGAGAGCCCGTGGTCGCCGTGGACGTAG Cookeina_indica_AF394029 ---GGGGGGGTCATGGTGGAGGA--GCG---------------CTTGC--TCCCCGCTAAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAG Cookeina_cremeirosea_AS142 ---GGGGGGGTCATGGTGGAGGA--GCGTTTGC----------------TTCCC-GCTTAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAG Cookeina_cremeirosea_AS210 ---GGGGGGGTCATGGTGGAGGA--GCGTTTGC----------------TTCCC-GCTTAAAGACATCTGGCGGAGAGTCCGTGGACGCCGTGGACGTAG Cookeina_speciosa_AF394018 -----GGGGGTCTTGGCGGAGGA--GCGCGCGCCCGACGGGCGCCGTC--TCCCCGCTCAAAGCCATCTGGCGGAGAGTCTGTGGTCGCCGTGGACGTCG Cookeina_speciosa_AF394010 C---GGGGGGTGTTGGCGGAGGA--GCGCG--CCCGACGGGCGCCGCC--TCCCCGCTCAAAGCCATCTGGCGGAAAGTCTGTGGTCGCCGTCGCCGTCG Cookeina_speciosa_AF394003 G----GGGGGTCTTGGCGGAGGA--GCGGGCGCCCGACGGGCGCCGCC--TCCCCGCTCAAAGCCATCTGGCGGAGAGTCTGGGGTCGCCGTGGACGTCG Microstoma_floccosum_AF394045 CGTCGTCGGTT-ATGGCGGAGAA-TGTG----CC-GTTGTG-GCACTC--TCCC-GCCCAAAGCCATCTGGCGGAGAGCCCTGGTCTGGCGCCGGCGTAG Microstoma_floccosum_AF394046 CGTCGTCGGTT-ATGGCGGAGAA-TGTG----CC-GTTGTG-GCACTC--TCCC-GCCCAAAGCCATCTGGCGGAGAGCCCTGGTCTGGCGCCGGCGTAG Cookeina_tricholoma_AF394023 TGAGATAC---TCTCGTCCG-----T-CGGCCCCGTCCGGCCC-------TCCCGCCGC----GA-CA--CCCC----AGAC-TT-CT--CGCG--ATT- Cookeina_tricholoma_AF394025 TGAGA--CAC-TCTCGTCCG-----T-CGGCCCCGTCCGGCCC-------TCCCGCCGC----GA-CA--CCCC----AGAC-TT-CT--CGCG--ATT- Cookeina_sinensis_AF394028 TGAGA--CGC-TCTCGTCCG-----T-CGGCCCCGCCCGGGCC-------TCCCGCCGC----GA-CA--CCCC----AGAC-TT-CT--CGCG--ATT- Cookeina_sinensis_AF394027 TGAGA--CGC-TCTCGTC-G-----T-CGGCCCCGCCCGGGCC-------TCC-GCCGC----CA-CA--CCCC----AGAC-TTACT--CGCG--ATT- Cookeina_colensoi_AF394532 TGAAAAACC--TCTCGACCGC---TT-GGCGCC----CCCAG-----TTATCCTGCCGC----GAACA-TAG-TTTTTCAACGAT-----------AT-G Cookeina_colensoi_AF394531 TGAAAAACC--TTTCGTCCGCC---T-GGCGCG----CCCAG-----TTATCCTGCCGC----GAACG-TAG-TTTTTCAACGAT-----------AT-G Cookeina_colensoi_AF394040 TGAAAAACC--TCTCGTCCGC---TT-GGCGCG----CCCAG-----TTATCCTGCCGC----GAACACA-G-TTTTTCAACGAT-----------AT-G Cookeina_colensoi_AF394038 TGAAAAACC--TCTCGTCCGC---TT-GGCGTG----CCCAG-----TTATCCTGCCGC----GAACGCA-G-TATCTCAACGAT-----------AT-G Cookeina_venezuelae_AF394041 TGAAACACC--TCTCGTCCAG----T-GGCGCG----CCCAG-----TTATCCTGCCG-T--GGA-CACA-GCTTT-CCAACC-------------ATT- Cookeina_venezuelae_AF394044 TGAAACACCCCTC--GTCCCG---TT-GGCGCA----CCCAG-----TTATCCTGCCGC----GAACACA-CCTTT-CCAACG-------------ATT- Cookeina_insititia_AF394032 TGAGACA---TTCTCGTCC-G---TTTGGCGTG----CCCGG-----TTATCCTGCCGC----GA-CG------TTT-CAA---T-CT--CGACCTATT- Cookeina_insititia_AF394031 TGAGACA---TTCTCGTCC-G---TTTGGCGTG----CCCGG-----TTATCCTGCCGC----GA-CG------TTT-CAAC-TT-----CGACCTATT- Cookeina_indica_AF394029 TGAGATA---TTCTCGTCCGG---TT-GGTGCT----CCCGG-----TTATCCTGCCG-TT--GAAGCTTGCTATTT---AT-CT-----------ATT- Cookeina_cremeirosea_AS142 TGAGATA---TTCTCGTCCGG---TT-GGTGCT----CCCGG-----TTATCTAGCCG-TT--GAAGCTTTGCATTTTT-AT-CT-----------ATT- Cookeina_cremeirosea_AS210 TGAGATA---TTCTCGTCCGG---TT-GGTGCT----CCCGG-----TTATCTAGCCG-TT--GAAGCTTTGCATTTTT-AT-CT-----------ATT- Cookeina_speciosa_AF394018 TGAGCATTCCAA-TCATCGTCC---T-GGCGGCGCGCCCCGG-----TTATCCAGCCG--T----A---------------------------------- Cookeina_speciosa_AF394010 TGAA----CATTCCAATC--A----T-CGTCCGACCGGTGCGCCGCG-------GCGG--T--CC--AGCCGTT-GACCT-CTGTTTTTTCTCGCGATT- Cookeina_speciosa_AF394003 TGAGCAATC--A-TCGTCCC-------GGCGCGCGCCCC-GG-----TTATCCAGCCG--TC-GA-CCG--CGTTTTT------------CCACCGATT- Microstoma_floccosum_AF394045 TAGG-----TTTCTCGTTAAACAC--TCGTCGGAGCCTGTGGTCAGGTTATCCAGCCGCGT--CAAGAACA-CTTT--CCATG--------------TT- Microstoma_floccosum_AF394046 TAGG-----TTTCTCGTTAAACAC--TCGTCGGAGCCTGTGGTCAGGTTATCCAGCCGCGT--CAAGAACA-CTTT--CCATG--------------TT- Cookeina_tricholoma_AF394023 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAACTTAAGCATATCAAT----------- Cookeina_tricholoma_AF394025 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAAC------------------------- Cookeina_sinensis_AF394028 GACCTCGGA-TCAGGTAGGGATACCCGC-TG---------------------------- Cookeina_sinensis_AF394027 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAA-------------------------- Cookeina_colensoi_AF394532 GACCTCGGA-TCAGGTAGGGATACCCG-------------------------------- Cookeina_colensoi_AF394531 GACCTCGGA-TCAGGTAGGGATACCC--------------------------------- Cookeina_colensoi_AF394040 GACCTCGGA-TCAGGTAGGGATACCCG-------------------------------- Cookeina_colensoi_AF394038 GACCTCGGA-TCAGGTAGGGATACCC--------------------------------- Cookeina_venezuelae_AF394041 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAACTTAAGCATATCAATAA--------- Cookeina_venezuelae_AF394044 GACCTCGGA-TCAGGTAGGGATACGCAACTTAAG-----CATATCAATAAGCCCGGGA- Cookeina_insititia_AF394032 GACCTCGGA-TCAGGTAGGGA-------------------------------------- Cookeina_insititia_AF394031 GACCTCGGA-TCAGGTAGGGATACCC--------------------------------- Cookeina_indica_AF394029 GACCTCGGA-TCAGGTAGGGATACCC--------------------------------- Cookeina_cremeirosea_AS142 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAACTTAAGCATATCAATAAGCGGAGGAA Cookeina_cremeirosea_AS210 GACCTCGGA-TCAGGTAGGGATAC-----T----------------------------- Cookeina_speciosa_AF394018 ----------------------------------------------------------- Cookeina_speciosa_AF394010 GACCTCGAAATCAGGTAG----------------------------------------- Cookeina_speciosa_AF394003 GACCTCGGA-TCAGGTAGGGACACCCGC-TGAACTTAAGCATATCAATAAGCCC----- Microstoma_floccosum_AF394045 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAACTTAAGCATATCAATAAGCCCCGG-- Microstoma_floccosum_AF394046 GACCTCGGA-TCAGGTAGGGATACCCGC-TGAACTTAAGCATATCAATA---------- ; END; begin mrbayes; Lset nst = 6 rates = gamma; set autoclose = yes; mcmcp ngen = 1000000 printfreq = 10 samplefreq = 100 nchains = 4 temp = 0.2 savebrlens = yes filename = testc; mcmc; sumt filename = testc contype = allcompat burnin = 2500; sump filename = testc nruns = 2 burnin = 2500 printtofile = Yes; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 759; END; BEGIN TREES; Title 'Trees from "testc.con"'; LINK Taxa = Taxa; TRANSLATE 1 Cookeina_tricholoma_AF394023, 2 Cookeina_tricholoma_AF394025, 3 Cookeina_sinensis_AF394028, 4 Cookeina_sinensis_AF394027, 5 Cookeina_colensoi_AF394532, 6 Cookeina_colensoi_AF394531, 7 Cookeina_colensoi_AF394040, 8 Cookeina_colensoi_AF394038, 9 Cookeina_venezuelae_AF394041, 10 Cookeina_venezuelae_AF394044, 11 Cookeina_insititia_AF394032, 12 Cookeina_insititia_AF394031, 13 Cookeina_indica_AF394029, 14 Cookeina_cremeirosea_AS142, 15 Cookeina_cremeirosea_AS210, 16 Cookeina_speciosa_AF394018, 17 Cookeina_speciosa_AF394010, 18 Cookeina_speciosa_AF394003, 19 Microstoma_floccosum_AF394045, 20 Microstoma_floccosum_AF394046; TREE con_all_compat = ((19:0.00185,20:0.001637)1.00:0.1623675,((18:0.064189,(16:0.044534,17:0.146655)0.63:0.022184)1.00:0.1968,(((1:0.002008,2:0.001891):0.025475,(3:0.002088,4:0.007669)1.00:0.043002)1.00:0.088986,((13:0.02698,(14:0.006551,15:0.002277)1.00:0.024929)1.00:0.065984,((11:0.017393,12:0.004305)1.00:0.068218,((9:0.043808,10:0.051902)0.98:0.022346,((5:0.012636,6:0.009398)1.00:0.016531,(7:0.008324,8:0.011845)0.77:0.004404)1.00:0.022434)1.00:0.075148)0.90:0.021335)0.46:0.018672)1.00:0.035162)0.41:0.1623675)[% ] [% ] [% setBetweenBits = selected ]; TREE con_all_compat = (1:0.002008,2:0.001891,((3:0.002088,4:0.007669):0.043002,((((((5:0.012636,6:0.009398):0.016531,(7:0.008324,8:0.011845):0.004404):0.022434,(9:0.043808,10:0.051902):0.022346):0.075148,(11:0.017393,12:0.004305):0.068218):0.021335,(13:0.02698,(14:0.006551,15:0.002277):0.024929):0.065984):0.018672,(((16:0.044534,17:0.146655):0.022184,18:0.064189):0.1968,(19:0.00185,20:0.001637):0.324735):0.035162):0.088986):0.025475); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 759; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 759; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1450203755868; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8200192873986025400; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4024558361154839080; mqVersion 275; checksumv 0 3 2335068742 null getNumChars 759 numChars 759 getNumTaxa 20 numTaxa 20 short true bits 15 states 15 sumSquaresStatesOnly 240281.0 sumSquares 240281.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 406; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 956 838; setLocation 340 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #8200192873986025400 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #8200192873986025400; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 550 771; setLocation 340 0; 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.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8200192873986025400 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 832.1450202867092.2656039606494804688; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 550 771; setLocation 340 0; 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.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; 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 #4024558361154839080 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 550 771; setLocation 340 0; 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; endTell; end;