#NEXUS [written Wed Jul 24 17:07:42 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=8; TAXLABELS Xylaria_venustula_GU300091_ Xylaria_oligotoma_GU300092_ Xylaria_arbuscula_AF163028_ Xylaria_striata_GU300089_ Xylaria_arbuscula_Var_plenofissura_GU339495_ F051 Xylaria_venosula_EF026149_ Xylaria_venosula_GU797434_ ; END; BEGIN CHARACTERS; TITLE XylariaMB; DIMENSIONS NCHAR=576; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Xylaria_venustula_GU300091_ TCCGTAGGTGAACCTGCGGAGGGATCATTAAAGAGTTTTT-ACAACTCCCTAAACCCATGTGAACTTACCATTTGTTGCCTCGGCAGGTC-GCGCTTAACCCCGTGAGACCCCTACCCTGTAGGG-CCTTACCCGGTGGACGCGGGCTT-CCCTGCCGGCGGCCCATCAAACTCTGTT--TTTATATTATATTTTACATCTGAATC-TATAACGGAATACGTTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTCTGTTGCTTAGTGTTAGGAGCCTACAG-----------CCCTCTGTAGCTCCCCAAAGTTAGTGGCGGAGTCGGTCTCACACTCTAGACGTAGTAAATCTTTTTTTTATCTCGCCTACAGA-GGAG-CCGGCGCCTTGCCGTAAAA-CCCCC-TCATTTTTTTTACAAGGTTGACCTCG Xylaria_oligotoma_GU300092_ TCCGTAGGTGAACCTGCGGAGGGATCATTAAAGAGTGTA--ACAACTCCC-AAACCCATGTGAACTTACCTTCTGTTGCCTCGGCAGGTC-GC-GCCTACCCTGTGAGA-CCCTACCCTGTAGAG-TCTTACCCGGTGGACGCGGGTAC-CCCTGCCGGCGGCCTACAAAACTCTGTT--TACTGATGTTATT-----TCTGAATC-TATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTTTGTTGCTTAGTGTTAGGAGCCTACAG-----------TCCTCTGTAGTTCCCTAAAGTTAGTGGCGGAGTCGGT-TCACACTCTAGACGTAGTAGA-----TTTTTATCTCGCCTATAAATGGA--CCGGCGTCCTGCCGTAAAA-CCCCCCTAA-TTTCT---CAAGGTTGACCTCG Xylaria_arbuscula_AF163028_ ------------CCAGCGGAGGGATCATTAAAGAGTTAATTACAACTCCC-AAACCCATGTGAACTTACCTTCTGTTGCCTCGGCAGGTC-GT-GTTTACCCTGTGAGG-TCCTACCCTGTAGG-ACCCTACCTGGTAGACACGGGTAC-GCCTGCCGGTGGCCCATGAAACTCTGTTAATTC-TATGTTA-------TCTGAATC-TATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCCCTGTTGCTTAGCGTTGGGAGCCTAC-G-----------CCTTCTGTAGCTCCCCAAAGTTAGTGGCGGAGTCGG--TCACACTCTAGACGTAGTAGATC-------TATCTCGTCTGTAG-TG-AGGCCGGTCCCCTGCCGTAAAA-CCCCCCTAA-TTTTT---AAAGGTTGACCTCG Xylaria_striata_GU300089_ TCCGTAGGTGAACCTGCGGAGGGATCATTAAAGAGTT-ATCATAACTCCC-AAACCCATGTGAACCTACCTT-TGTTGCCTCGGCAAGTCTGCAGTTTACCCTGTGAGA-CCCTACCCTGTAGGGACCTTACCCGGTAATTGCAGGTAAAGCCTGCCGGTGGTCTATTAAACTCTGTT--TAC-TATGTTAT------TCTGAATCATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCCTTGTTGCTTAGCGTTGGGAGCTTACAGAAA--------CCTTTTGTAGTTCCTTAAAGTTAGTGGCAGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTTATCTCGCCTATAGATG-AG-CCGGTCTTTTGCCGTAAAA-CCCC-TTAA-TCTTT---AAAGGTTGACCTCG Xylaria_arbuscula_Var_plenofissura_GU339495_ TCCGTAGGTGAACCTGCGGAGGGATCATTAAAGAGTT-AT-ACAACTCCT-AAACCCATGTGAACCTACCAT-TGTTGCCTCGGCAGGTCTGCAGCTTACCCTGTAAGA-CCCTACCCTGTAGGGACCTTACCCGGTAGTTGCGGGCATAACCTGCCGGTGGTCTACCAAACTCTGTT--TAC-TATGTTAT------TCTGAATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCCCTGTTGCTTAGCGTTGGGAGCCTACAGATAGATATCTACCTTCTGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTTATCTCGCCTATAGATG-AG-CCGGTCCCCTGCCGTAAAA-CCCCC-TAATTTTTT---AAAGGTTGACCTCG F051 ---------------GCGGAGGGATCATTAAAGAGTTAA-AACAACTCCT-AAACCCATGTGAACCTACCAT-TGTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGAACTTACCCGGTAGTTGCGGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT--TAC-TATGTTAT------TCTGAATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGTCTACAGATA--------CCCTCTGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTTATCTCGCCTATAGATG-AG-CCGGTCCCTTGCCGTAAAAACCCC--TAA-TTTCT---AAAGGTTGACCTCG Xylaria_venosula_EF026149_ TCCGTAGGTGAACCTGCGGAGGGATCATTAAAGAGTTAA-AACAACTCCT-AAACCCATGTGAACCTACCAT-TGTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGACCTTACCCGGTAGTTGCCGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT--TAC-TATGTTAT------TCTGAATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGCCTACAGATA--------CCCTCTGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTTATCTCGCCTATAGATG-AG-CCGGTCCCTTGCCGTAAAAACCCC--TAA-TTTCT---AAAGGTTGACCTCG Xylaria_venosula_GU797434_ ------GGTGAACCTGCGGAGGGATCATTAAAGAGTTAA--ACAACTCCT-AAACCCATGTGAACCTACCTT-TGTTGCCTCGGCAGGTCTGCAACTTACCCTGAGGGG-ACCTACCCTGTAGGGACCTTACCCGGTAGTTGCCGGCATAACCTGCCGGTGGTCTACTAAACTCTGTT--TAC-TATGTTAT------TCTGAATAATATAACTAAATAAG-TTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCC-CTGTTGCTTAGCGTTGGGAGCCTACAGATA?-------CCCTCTGTAGTTCCTTAAAGTTAGTGGCGGAGTCGGTTTCACACTCTAGACGTAGTAAA------TTTTATCTCGCCTATAGATG-AG-CCGGTCCCTTGCCGTAAAA-CCCCC-TAA-TTTCT---AAAGGTTGACCTCG ; END; BEGIN TREES; Title XylariaMB; LINK Taxa = Taxa; TRANSLATE 1 Xylaria_venustula_GU300091_, 2 Xylaria_oligotoma_GU300092_, 3 Xylaria_arbuscula_AF163028_, 4 Xylaria_striata_GU300089_, 5 Xylaria_arbuscula_Var_plenofissura_GU339495_, 6 F051, 7 Xylaria_venosula_EF026149_, 8 Xylaria_venosula_GU797434_; TREE con_50_majrule = (1:0.074387,2:0.038924,(3:0.044684,(4:0.042076,(5:0.00589,(6:0.006548,(7:0.002075,8:0.004135)0.96:0.004405)1.00:0.022425)0.99:0.019186)0.94:0.021604)1.00:0.036802); TREE con_50_majrule = (1:0.074387,2:0.038924,(3:0.044684,(4:0.042076,(5:0.00589,(6:0.006548,(7:0.002075,8:0.004135):0.004405):0.022425):0.019186):0.021604):0.036802); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 576; 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 - 576; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 576; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374685663072; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6924655309076338036; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5745608279000583105; mqVersion 275; checksumv 0 3 4083366795 null getNumChars 576 numChars 576 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 98699.0 sumSquares 98699.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 246; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1153 678; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6924655309076338036 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6924655309076338036; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 611; 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 #6924655309076338036 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1310161057058.2853344341899662354; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 611; 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 off; 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 2; setTree '(1:0.0371935,(2:0.038924,(3:0.044684,(4:0.042076,(5:0.00589,(6:0.006548,(7:0.002075,8:0.004135):0.004405):0.022425):0.019186):0.021604):0.036802):0.0371935);'; 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 #5745608279000583105 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 907 611; 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;