#NEXUS [written Wed Jul 24 16:36:55 GMT+00:00 2013 by Mesquite version 2.75 (build 566) at Macintosh-6.local/192.168.5.142] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=11; TAXLABELS Chaetosphaeria_ovoidea_AF064641_ Striatosphaeria_codinaeophora_AF178546_ Chaetosphaeria_aterrima_AF178565_ Camarops_microspora_AY083821_ Camarops_petersii_AY346265_ Erythromada_lanciospora_DQ231442_ F365 Chaetosphaeria_curvispora_GU180636_ Chaetosphaeria_ciliata_GU180637_ Lasiosphaeriella_noonae_daniae_HM171284__ Leptosporella_gregaria_HM171289_ ; END; BEGIN CHARACTERS; TITLE LeptosporellaMB; DIMENSIONS NCHAR=477; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Chaetosphaeria_ovoidea_AF064641_ -------------------------------------------------------TGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CC-AGGCCCGAGTTGTAATTTGCAGAGGATGCTTCCGGTGCGGCGCCGTCCAAGTCCCCTGGAACGGGGTGCCACAGAGGGTGAGAGCCCCGTCGGGTCGGCCG-CCAAGCCTATGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAGACCCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAAACTTGCGCCGGGC-GTTCAGCGGGCGTTCT-CGCCCGTGCACTCGCCCCGGCGCAGGCCAACGTCGG Striatosphaeria_codinaeophora_AF178546_ ATA?CCGCTGAACTTAAGCATATCAATAAGC?GAG?AAAAGAAACCAACATGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CC--GGCCCGAGTTGTAATTTGCAGAGGATGCTTCCGGCAACGCGCCTTCCAAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTCCGGTCGGCCG-CCGCGCCTGTGCGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAACGGGAGGTAGACCCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTCGGGACCAGACGTGCGCCGGGC-GTTCAGCGGGCGTTCT-CGCCCGTGTACTCGCCCCGGCGCAGGCCAGCGTCGG Chaetosphaeria_aterrima_AF178565_ ATACCCGCTGAACTTAAGCATATCAATAAGCGGAG?AAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CC-AGGCCCGAGTTGTAATTTGCAGAGGATGCTTTGGGCGCGGTGCCTTCCGAGTCCCCTGGAACGGGACGCCATAGAGGGTGAGAGCCCCGTCTGGTCGGACA-CCAAGCCTCTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTATATGTCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGAGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGTTCATGACCAGACTTGGACCG-GTCAATCATCCAGCGTTCT-CGCTGGTGCACTTTTCCCGGTCCAGGCCAGCATCAG Camarops_microspora_AY083821_ ----------------------------------------GAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CC--GGCCCGAGTTGTAATTTGCAGAGGACGCTTCTGGCGCGGTGCCTCCCGAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTATGGCAGGACA-CCTAGCCTGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACTTGCGCGGGGCCGATCATCCGGTGTTCT-CACCGGTGCACTCGGCCCGGCTCAGGCCAGCATCGG Camarops_petersii_AY346265_ -------CTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CC--GGCCCGAGTTGTAATTTGCAGAGGATGCTTTTGGCGCGGCGCCTCCCGAGTTCCCTGGAACGGGACGCCACAGAGGGTGAGAGCCCCGTATGGTAGGACG-CCTAGCCTGTGTAAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACTTGCGCCGGGCCGATCATCCGGTGTTCT-CACCGGTGCACTCGGCCCGGCTCAGGCCAGCATCGG Erythromada_lanciospora_DQ231442_ GTACCCGCTGAACTTAAGCATATCAATAAGCGCAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAGATTTGAAAGC-GCCCGCC-AGGA-CGCGTTGTAATCTGTAGAGGACGCTTCGGGCGACGCCCCGCCTAAGTCCCCTGGAACGGGGCGCCACAGAGGGTGAGAGCCCCGTGAGG-CGG-CGGCCGGTCCCGCGTGAAGCTCCCTCGACGAGTCGAGTAGTTTGGGATTGCTGCTCTAAATGGGAGGTACATTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGCTGAAAGGGAAGCGCTCGTGACCAGACTTGCGCGGGCGCGATCATCCGGCGTTCT-CGCCGGTGCCCTCGCGCCCGCTCAGGCCAGCGTCGG F365 ATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCTCTC-GGGCCCGAGTTGTAATTTGTAGAGGATGCTTCGGGCGCGGCGCCTTCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTACGGTTGGATG-CCTAGCCCGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAGTTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCTCGTGACCAGACGCGCGCCGGGCGGATCATCCAGCGTTCT-CGCTGGTGCACTCCGCCCGGCGCGGGCCAGCGTCGG Chaetosphaeria_curvispora_GU180636_ ATACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-TC--GGCCCGAGTTGTAATTTGTAGAGGATGCTTCGGGCGCGGCGCCTTCCAAGTCCCCTGGAACGGGGCGCCAGAGAGGGTGAGAGCCCCGTACTGTCGGCCG-CCAAGCCTGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAGACCCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACTTGCGCCGGGCCGATCATCTGGCGTTCT-CGCCAGTGCACTCGACCCGGCTCAGGCCAGCGTCGG Chaetosphaeria_ciliata_GU180637_ ---------------------------------------------------------CCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCT--AGGCCCGAGTTGTAATTTGCAGAGGATGCTTCCGGTGCGGCGCCGTCCAAGTCCCCTGGAACGGGGTGCCATAGAGGGTGAGAGCCCCGTCGGGTCGGCCG-CCAAGCCTATGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAGACCCCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACGTGCGCCGGGT-GTTCAGCGGGCGTTCT-CGCCCGTCTATTCGCCCTGGCGCAGGCCAGCGTCGG Lasiosphaeriella_noonae_daniae_HM171284__ GTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCCGGCC-CC--CGCCGGAGTTGTAATTTGGAGAGGACGCTTCTGGCGAGGCGCCGTCCAAGTCCCCAGGAACGGGGCGCCGCGGAGGGTGAGAGCCCCGTACGGTCGGACG-CCGAGCCTGTGCGAAGCTCCCTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAACGGGAGGTACGTTCCTTCTAAGGCTAAATACCGGCCGGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGGAAAGAGGGTCAAACAGCACGTGAAATTGTTGAAAGGGAAGCGCTCGTGACCAGACGCGCGCCTCGCCGATCCGCCAGCGCTCGCCGCTGGCGCCCTCGGCGCGGCGCGGGCCAGCGTCGG Leptosporella_gregaria_HM171289_ GTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCCTAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCC-CCCGGGCCCGAGTTGTAATTTGCAGAGGATGCTTCGGGCGCGGTGCCTTCCGAGTCCCCTGGAACGGGGCGCCATAGAGGGTGAGAGCCCCGTACGGTTGGACG-CCTAGCCCGTGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCAAAATGGGAGGTAAGTTCCTTCTAAAGCTAAATACCGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAATAGCACGTGAAATTGCTGAAAGGGAAGCGCTCGTGACCAGACGCGCGCCGGGCGGATCATCCAGCGTTCT-CGCTGGTGCACTCCGCCCGGCGCGGGCCAGCGTCGG ; END; BEGIN TREES; Title LeptosporellaMB; LINK Taxa = Taxa; TRANSLATE 1 Chaetosphaeria_ovoidea_AF064641_, 2 Striatosphaeria_codinaeophora_AF178546_, 3 Chaetosphaeria_aterrima_AF178565_, 4 Camarops_microspora_AY083821_, 5 Camarops_petersii_AY346265_, 6 Erythromada_lanciospora_DQ231442_, 7 F365, 8 Chaetosphaeria_curvispora_GU180636_, 9 Chaetosphaeria_ciliata_GU180637_, 10 Lasiosphaeriella_noonae_daniae_HM171284__, 11 Leptosporella_gregaria_HM171289_; TREE con_50_majrule = (1:0.009512,9:0.026278,(2:0.028548,(3:0.082779,((4:0.014808,5:0.014727)1.00:0.021145,((7:0.012887,11:0.005696)0.99:0.023158,10:0.101079)0.97:0.025028)0.71:0.014528,6:0.113479,8:0.021924)1.00:0.032417)1.00:0.018524); TREE con_50_majrule = (1:0.009512,9:0.026278,(2:0.028548,(3:0.082779,((4:0.014808,5:0.014727):0.021145,((7:0.012887,11:0.005696):0.023158,10:0.101079):0.025028):0.014528,6:0.113479,8:0.021924):0.032417):0.018524); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 477; END; begin mrbayes; set autoclose = no nowarn = yes; lset nst = 6 rates = gamma; unlink statefreq = ( all ) revmat = ( all ) shape = ( all ) pinvar = ( all ); prset applyto = ( all ) ratepr = variable; mcmcp ngen = 10000000 relburnin = yes burninfrac = 0.25 printfreq = 1000 samplefreq = 1000 nchains = 4 savebrlens = yes; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 477; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 477; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374683815113; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5077664827761468308; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2671104591479351971; mqVersion 275; checksumv 0 3 1659912115 null getNumChars 477 numChars 477 getNumTaxa 11 numTaxa 11 short true bits 15 states 15 sumSquaresStatesOnly 89857.0 sumSquares 89857.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 139; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #5077664827761468308 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #5077664827761468308; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 561 397; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; 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 #5077664827761468308 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1311448870136.7957320765020107954; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 561 397; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 1; orientRight; 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; setTree '((4:0.014808,5:0.014727)1.00:0.0105725,((10:0.101079,(7:0.012887,11:0.005696)0.99:0.023158)0.97:0.025028,(3:0.082779,6:0.113479,8:0.021924,(2:0.028548,(1:0.009512,9:0.026278):0.018524)1.00:0.032417)1.00:0.014528)0.71:0.0105725);'; 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 #2671104591479351971 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 561 397; setLocation 8 22; 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.chromaseq.ColorQuality.ColorQuality; tell It; toggleAmbiguities on; toggleMarks on; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; getEmployee #mesquite.chromaseq.SourceFileInfoEditor.SourceFileInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;