#NEXUS [written Sat Feb 11 12:27:42 CET 2017 by Mesquite version 3.0 (build 644) at VAIOMARGARITA/192.168.0.104] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=11; TAXLABELS Pyricularia_bothriochloae_KF777186_ Pyricularia_angulata_JF719830_ _Neocordana_musicola_CPC11225 Neocordana_musicola_CPC11228 Neocordana_musicola_CPC15987 Neocordana_musae_CPC16362 Neocordana_musae_CPC19065 Neocordana_musae_CPC16298 Neocordana_musae_CPC18127 Neocordana_musae_CPC17237 Neocordana_musae_CPC17293 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=521; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pyricularia_bothriochloae_KF777186_ AGGGATCATTACTGAGTTGCAAAACTCC-AACCCA-TGTGAAC-ATACCTTC-AACCGTTGCTTCGGCGGGTCCGCCCGCCGGAGGTAC---CAAACTCTTGAATTTTACAGGCGTCT-CTGAGCAAA-AAAACAAAATAA-TCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAGGCCCCCCGGGGCCTGGTGTTGGGGCGCCAGGGAGAACCCTAGCGGGTGCCCTGGGCCCCCAAGTCCATCGGCGGTCTCGTCGGTACGCCGAGCGCAGTAA-GACGCGGTAAAACGCG----CCCCTCGCCCGGACCGTAACGTCCTGCAC--CTGCCGCTAAA---CCCCCCA----AAATCTAAAGGTTGACCTCGGATCAGGTAGG Pyricularia_angulata_JF719830_ AGGGATCTAATCTGAGTTGAAAAACTCC-AACCCC-TGTGAAC-ACAACCTC-TGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTC---CAAACTCTT-ATTTTTACAG-TATCT-CTGAGCCTA-AAAGACAAATAA-TCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTC----GGCTTGGTGTTGGGGCGCCCGGGT---CCTCCGCGG---CCCGGGGCCCCCAAATCCATCGGCGGGCTCGTCGGTACACTGAGCGCAGTAA-AACGCGGTAAAACGCG----AACCTCGTTCGGACCGTCCCGGCGCGCAC--CAGCCGCTAAA---CCCCC-A----ATTTTTAAAGGTTGACCTCGGATCAGGTAGG _Neocordana_musicola_CPC11225 AGGGATCATTACAGAGTTGCAAAACTCC-AACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCACGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCACTCCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGCAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGACAAAGGT-GACCTCGGATCAG-TAGA Neocordana_musicola_CPC11228 AGGGATCATTACAGAGTTGCAATACTCC-AACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCACGTTTTCC-AGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCACTCCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGCAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGGTAAAGAGACCCCAACGGGAACGACAAAGGT-GACCTCGGATCAGGTAG- Neocordana_musicola_CPC15987 AGGGATCATTACAGAGTTGCAAAACTCC-AACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCACGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCACTCCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGCAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGACAAAGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC16362 AGGGATCATTACAGAGTTGCAAAACTCCCAACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGATAAAGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC19065 AGGGATCATTACAGAGTTGCAAAACTCC-AACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACTCCAGCCGCTAAAGAGACCCCAACGGGAACGATAAAGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC16298 AGGGATCATTACAGAGTTGCAAAACTCCCAACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGATAAAGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC18127 AGGGATCATTACAGAGTTGCAAAACTCCCAACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACCATAAGGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC17237 AGGGATCATTACAGAGTTGCAAAACTCCCAACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGATAAAGGTTGACCTCGGATCAGGTAGG Neocordana_musae_CPC17293 AGGGATCATTACAGAGTTGCAAAACTCCCAACCCTTTGTGAACCACAACCTCCAGTCGTTGCTTCGGCGGGCCCGCCCGCCGGAGGTTCAAACAAACTCATGTTTTCCGAGTACGTCTTCTGAGCAAACAAGAAAAAATAAATCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCCGCTTCGGCTTGGTGTTGGGGCGCCCGGGGC--TCCCAGCGGGC-CCCGGGGCCCCCAAGTTCATCGGCGGGCTCGTCGGAACCCTGAGCGTAGTAGCAAGGCCCTAAGAAGCCGAACCCCCTCGCTCGGCCCGTCCCGGCGTGCACACCAGCCGCTAAAGAGACCCCAACGGGAACGATAAAGGTTGACCTCGGATCAGGTAGG ; charset locus1 = 1 - 521; log start filename = mydata.log; END; begin mrbayes; outgroup KF777186_Pyricularia_bothriochloae_CPC21650; prset applyto = ( 1 ) statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); lset applyto = ( 1 ) nst = 6 rates = invgamma; unlink shape = ( all ) pinvar = ( all ) statefreq = ( all ) revmat = ( all ); mcmcp ngen = 100000000 relburnin = yes burninfrac = 0.25 printfreq = 1000 temp = 0.15 samplefreq = 1000 nchains = 4 savebrlens = yes stoprule = yes stopval = 0.01; mcmc; sumt; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 521; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 521; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 521; END; BEGIN TREES; Title 'Trees from "alignmrbayes.nex.con.tre"'; LINK Taxa = Taxa; TRANSLATE [0] 1 Pyricularia_bothriochloae_KF777186_, [1] 2 Pyricularia_angulata_JF719830_, [2] 3 _Neocordana_musicola_CPC11225, [3] 4 Neocordana_musicola_CPC11228, [4] 5 Neocordana_musicola_CPC15987, [5] 6 Neocordana_musae_CPC16362, [6] 7 Neocordana_musae_CPC19065, [7] 8 Neocordana_musae_CPC16298, [8] 9 Neocordana_musae_CPC18127, [9] 10 Neocordana_musae_CPC17237, [10] 11 Neocordana_musae_CPC17293; TREE con_50_majrule = (1:0.078919,2:0.061581,((3:0.003981,4:0.006252,5:0.00221)0.96:0.01078,6:0.002258,7:0.004016,8:0.002145,9:0.005956,10:0.002182,11:0.002198)1.00:0.093756); TREE con_50_majrule = (1:0.078919,2:0.061581,((3:0.003981,4:0.006252,5:0.00221):0.01078,6:0.002258,7:0.004016,8:0.002145,9:0.005956,10:0.002182,11:0.002198):0.093756); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1486812462922; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 8352690547825237051; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 632565080596120609; mqVersion 300; checksumv 0 3 2483031061 null getNumChars 521 numChars 521 getNumTaxa 11 numTaxa 11 short true bits 15 states 15 sumSquaresStatesOnly 101043.0 sumSquares 101043.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 271; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1111 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8352690547825237051 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1058.1486811700546.1381489158345311256; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 840 392; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.treefarm.MakeRerootings.AllRerootToolExtra.allRerootings; 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; 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 #632565080596120609 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 316; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 840 392; setLocation 8 8; 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.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;