#NEXUS [written Tue Nov 20 10:39:53 EST 2012 by Mesquite version 2.75 (build 566) at g-d25fn1r9dhjv/10.78.17.4] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS Minutisphaera_fimbriatispora_G155_a_ITS5_4 Minutisphaera_fimbriatispora_G155_b_ITS5_4 Minutisphaera_sp_G156_1 Minutisphaera_japonica_JCM_18561 Minutisphaera_japonica_JCM18562 Minutisphaera_japonica_JCM_18560 Minutisphaera_fimbriatispora_A242_7d Minutisphaera_fimbriatispora_A242_7c Minutisphaera_sp_G156_2a Minutisphaera_sp_G156_2b ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=605; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Minutisphaera_fimbriatispora_G155_a_ITS5_4 TTCGCTAGGTGAACCGAAGGATCATTAAAAAAAAGTTGTGTGAGGCGGTGTCCTGGCAGACCCATGTAGCCGCTTATACATCAACACCCTCTGTATATCTACCGTGTTGCTTTGGCGGGACGGCAACCC----------------AGTTGTCCGCAGGACCTGTTAAGGCCCCGCGAGTGCCCGCCGGAGAACCACCAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCCGCCCCC-TGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGCAAACGGCACTCTAGCGTAGTAGAAATTAACTCGCTGGGGACCGGGGCTTGGGTAGCTGTTAAACACGCGTCTCTGGCGCACATCTTAAGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_fimbriatispora_G155_b_ITS5_4 TTCCGTAGATCGAAMGRAGGATCATTAAAAAAAAGTTGTGTGAGGCGGTGTCCTGGCAGTGCCAGGTAGCCGCTTATACATCAACACCCTCTGTATATCTACCGTGTTGCTTTGGCGGGACGGCAACCC----------------AGTTGTCCGCAGGACCTGTTAAGGCCCCGCGAGTGCCCGCCGGAGAACCACCAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCCGCCCCC-TGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGCAAACGGCACTCTAGCGTAGTAGAAATTAACTCGCTGGGGACCGGGGCTTGGGTAGCTGTTAAACACGCGTCTCTGGCGCACATCTTAAGGTTGACCTCGGATAAGGTAGRGATACCCGCTGAACTTAAA Minutisphaera_sp_G156_1 TTCCGTAGGTGAACCGAAGGATCATTAAAAAAAAGTTGTGCGAGGCGGCC-CCAGGCACTGCCAGGTGGCCGCTTAGACATCAACACCCTCTGTATATCTACCGCGTTGCTTTGGCGGGACGGCAG-CCATCAGCTCCGCTGGGAAGCTGTCCGCAGGGCCTCTTAAAGCCCCGCGAGTGCCCGCCAGAGAACCACCAAACACATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCCGCCTCCATGTGGGCGGGCCTCAAAGTTATCAGCGGCTGAGCGAACGGTATTCCAGCGTAGTAGAAATTAACTCGCTGGGGACCCGGCCTCAGGTAGCTGTCGAACACACGCCTTTGGCGTATATTTTAAGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_japonica_JCM_18561 ---------???ACCGAAGGATCATT---AAAAGTTTGTTCGAGGCGGTC-CCAGGCACTGCCAGGTGGCCGCTTAGACATCAACACCCTCTGTATATCTACCGCGTTGCTTTGGTGGGACGGCAG-CCAGCAGCCCTGCTGGGAAGCTGTCCGCAGGGCCTCTTAAGGCCCCGCGAGCGCCTGCCAGAGAACCGTTAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCTGTCTCCACGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGAGAACGGCGTTCTAGCGTAGTAGAAATTAACTCGCTGGGGACC-GGCCTCAGGTAGCTGTCAAATCCGCGCCTTT-GCGCACATCT???----------------------------------------- Minutisphaera_japonica_JCM18562 ---------???ACCGAAGGATCATT---AAAAGTTTGTTCGAGGCGGTC-CCAGGCACTGCCAGGTGGCCGCTTAGACATCAACACCCTCTGTATATCTACCGCGTTGCTTTGGTGGGACGGCAG-CCAGCAGCCCTGCTGGGAAGCTGTCCGCAGGGCCTCTTAAGGCCCCGCGAGCGCCTGCCAGAGAACCTTTAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCTGTCTCCACGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGAGAACGGCGTTCTAGCGTAGTAGAAATTAACTCGCTGGGGACC-GGCCTCAGGTAGCTGTCAAATCCGCGCCTTT-GCGCACATCTT-AGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_japonica_JCM_18560 ---------???ACCGAAGGATCATT---AAAAGTTTGTTCGAGGCGGTC-CCAGGCACTGCCAGGTGGCCGCTTAGACATCAACACCCTCTGTATATCTACCGCGTTGCTTTGGTGGGACGGCAG-CCAGCAGCCCTGCTGGGAAGCTGTCCGCAGGGCCTCTTAAGGCCCCGCGAGCGCCTGCCAGAGAACCTTTAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCTGTCTCCACGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGAGAACGGCGTTCTAGCGTAGTAGAAATTAACTCGCTGGGGACC-GGCCTCAGGTAGCTGTCAAATCCGCGCCTTT-GCGCACATCTT-AGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_fimbriatispora_A242_7d TTCCGTAGGTGAACCGAAGGATCATTAAAAAAAAGTTGTGTGAGGCGGTAACCTGGCAGTGCCAGGTGGCCGCTTATACATCAACACCCTCTGTATATCTACCGTGTTGCTTTGGCGGGACGGCAACCCATCAGCTCCGCTGGGAAGTTGTCCGCAGGGCCTGTAAAGGCCCCGCGAGCGCCCGCCGGAGAACCACCAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCTGCCCCCCTGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGCAAACGGCACTCTAGCGTAGTAGAAATTAACTCGCTGGGGACCGGGGCTCAGGCAGCTGTTAAACACGCGTCTCTGGCGCACATCTTAAGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_fimbriatispora_A242_7c TTCCGTAGGTGAACCGAAGGATCATTAAAAAAAAGTTGTGTGAGGCGGTAACCTGGCAGTGCCAGGTGGCCGCTTATACATCAACACCCTCTGTATATCTACCGTGTTGCTTTGGCGGGACGGCAACCCATCAGCTCCGCTGGGAAGTTGTCCGCAGGGCCTGTAAAGGCCCCGCGAGCGCCCGCCGGAGAACCACCAAACTCATGTTAAACCGTGATGTCTGAGCTTTACAAGCAATAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCCTTGGTATTCCGAGGGGCATGCCTTTTCGAGCGTCATTACAACCGTCAAGCTCTGCTTGGTATTGGGCCTCTGCCCCCCTGTGGGCGGGCCTTAAAGTCATCAGCGGCTGAGCAAACGGCACTCTAGCGTAGTAGAAATTAACTCGCTGGGGACCGGGGCTCAGGCAGCTGTTAAACACGCGTCTCTGGCGCACATCTTAAGGTTGACCTCGGATAAGGTAGGGATACCCGCTGAACTTAAA Minutisphaera_sp_G156_2a ttccgaaggtgaaccgaaggatcattaaaaaaacgttgtgtgaggcggccaccgggcaatgccagttggccgcttagacatcaacaccctctgtatatctaccgtgttgctttggcgggacgacaacccatcagctccgctgggaagttgtccgcagggcctgttaatgccccgcgagcgcccgccagagaaccaccaaacacatgttaaaccgtgatgtctgagctttacaagcaataagttaaaactttcaacaacggatctcttggttctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcatattgcgccccttggtattccgaggggcatgccttttcgagcgtcattacaaccgtcaagctctgcttggtattgggccttcgtccctgtgtgggcgggcctcaaagtcatcagcggctgagtaaacggcactctagcgtagtagaaattaactcgctggggacc-ggacttaggcagctgttaaacacgcgcctctggcgcatatcttcaggttgacctcggataaggtagggatacccgctgaacttaa- Minutisphaera_sp_G156_2b KtYcgtaggtgaaccgaaggatcattaaaaaaacgttgtgtgaggcggccaccgggcaatgccagttggccgcttagacatcaacaccctctgtatatctaccgtgttgctttggcgggacgacaacccatcagctccgctgggaagttgtccgcagggcctgttaatgccccgcgagcgcccgccagagaaccaccaaacacatgttaaaccgtgatgtctgagctttacaagcaataagttaaaactttcaacaacggatctcttggttctcgcatcgatgaagaacgcagcgaaatgcgataagtaatgtgaattgcagaattcagtgaatcatcgaatctttgaacgcatattgcgccccttggtattccgaggggcatgccttttcgagcgtcattacaaccgtcaagctctgcttggtattgggccttcgtccctgtgtgggcgggcctcaaagtcatcagcggctgagtaaacggcactctagcgtagtagaaattaactcgctggggacc-ggacttaggcagctgttaaacacgcgcctctggcgcatatcttcaggttgacctcggataaggtagggatacccgctgaacttaa- ; END; BEGIN MacClade; Version 4.0 87; LastModified -858717025; FileSettings editor '0' '0' '1' '1'; Singles 100; Editor 00011001111111100100010010 '1' '12' Geneva '9' '100' '1' all; EditorPosition '46' '6' '1363' '2499'; TreeWindowPosition '46' '6' '1371' '2510'; ListWindow Characters closed Geneva '9' '50' '10' '129' '399' 000; ListWindow Taxa closed Geneva '9' '50' '10' '129' '490' 100000000; ListWindow Trees closed Geneva '9' '50' '10' '276' '490'; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ListWindow ExSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharSets closed Geneva '9' '50' '10' '276' '490'; ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ChartWindowPosition '52' '30' '1358' '2500'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder; OtherSymbols & / 00 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '1251' '46' '115' '165'; TreeWindowProgram 10; TreeWindow 0000; Continuous '0' '3' 1; Calculations 0000001; SummaryMode '0' '0' 0; Charts Geneva '9' ( normal ) 0010; NexusOptions '0' '0' '50' 001011001; TipLabel '1'; TreeFont Geneva '9' ( normal ); TreeShape 1.0 1.0 0100; TraceLabels 0101; ChartColors '0' '0' '65535' '9' '0' 1; ChartBiggestSpot 1; ChartPercent 10; ChartBarWidth '10' 1; ChartVerticalAxis 10101; ChartMinMax '0'; TraceAllChangesDisplay '1' 1; BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101; ContinuousBranchLabels 0; AllStatesBranchLabels 1; IndexNotation '2' 1; PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '0' '0' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000; MatchChar 00 .; EntryInterpretation 01; ColorOptions 00; TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110; EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '1' 100010101110011; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010; BothTools '1'; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 605; END; BEGIN CODONS; CODONPOSSET * UNTITLED = N: 1- 605 ; CODONPOSSET CodonPositions = N: 1- 605 ; CODESET * UNTITLED = universal: 1 - 605; END; BEGIN TREES; Title 'Trees from "ITS_tree."'; LINK Taxa = Taxa; TRANSLATE 1 Minutisphaera_fimbriatispora_G155_a_ITS5_4, 2 Minutisphaera_fimbriatispora_G155_b_ITS5_4, 3 Minutisphaera_sp_G156_1, 4 Minutisphaera_japonica_JCM_18561, 5 Minutisphaera_japonica_JCM18562, 6 Minutisphaera_japonica_JCM_18560, 7 Minutisphaera_fimbriatispora_A242_7d, 8 Minutisphaera_fimbriatispora_A242_7c, 9 Minutisphaera_sp_G156_2a, 10 Minutisphaera_sp_G156_2b; TREE tree_1 = (((2:0.00815,1:0.01051)0.93:0.01523,(8:0.0,7:0.0)0.80:0.00572)0.93:0.02187,(10:0.0,9:0.00188)0.96:0.0294,(3:0.02148,(4:0.0,(5:0.0,6:0.0)0.74:0.00198)1.00:0.05425)0.97:0.03674):0.0; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 605; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1353425993266; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5600502203505025376; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3462702141750548908; mqVersion 275; checksumv 0 3 2800717677 null getNumChars 605 numChars 605 getNumTaxa 10 numTaxa 10 short true bits 3458764513820540943 states 15 sumSquaresStatesOnly 122245.0 sumSquares -7.540106640128779E20 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;