#NEXUS [written Wed Jul 24 16:48:44 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=10; TAXLABELS Pestalotiopsis_funerea_OG_EF055197_ Pestalotiopsis_bicilia_OG_AF409973_ F121_ Pestalotiopsis_theae_HQ832793_ Pestalotiopsis_versicolor_AF409993_ Pestalotiopsis_sinensis_AF409966_ F003_ Pestalotiopsis_sydowiana_HM190154_ Pestalotiopsis_aquatica_AF409956_ Pestalotiopsis_longisetula_AF409971_ ; END; BEGIN CHARACTERS; TITLE PestalotiopsisMB; DIMENSIONS NCHAR=573; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pestalotiopsis_funerea_OG_EF055197_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACC-ATTGTTGCCTCGGCAGAAGCTACCT-GGT-TACCCTACCTTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGA-ACGGCCTACCCTGTAACGGCTGCCGGTGGACTACCAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAGCCTACCGCTTTTGCTAGCGGTAGCTCCTGAAATACAACGGCGGATCTGCGATATCCTCTGAGCGTAGTAA-TTTTTA-TCTCGCTTTTGACTGGAGTTGCAGCGTCTTTAGCCGCTAAACCCCCCAAATTTTTTAATGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT Pestalotiopsis_bicilia_OG_AF409973_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACC-ATTGTTGCCTCGGCAGAAGCT-GCTCGGTGCACCCTACCTTGGAACGGCCTACCCTGTAGCGCCTTACCCTGGA-ACGGCTTACCCTGTAACGGCTGCCGGTGGACTACCAAACTCTTGTTATTTTATTGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAGCCTACTGCTTTTGCTAGCTGTAGCTCCTGAAATACAACGGCGGATCTGCGATATCCTCTGAGCGTAGTAAATTTTTA-TCTCGCTTTTGACTGGAGTTGCAGCGTCTTTGGCCGCTAAATCCCCCAA--TTTTTAATGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT F121_ -----GATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAGGTTACCT-GGT-------------------------------------ACC-TGGAGACAGGTTACCCTGTAGCAACTGCCGGTGGACTACTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATTTACAGTTAT--------GTAATTCCTGAAATACAACGGCGGATCTGTGGTATCCTCTGAGCGTAGTAAATTATT--TCTCGCTTTTGTTAGGTGCTGCAGCTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT Pestalotiopsis_theae_HQ832793_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAGGTTACCT-GGT-------------------------------------ACC-TGGAGACAGGTTACCCTGTAGCAGCTGCCGGTGGACTACTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATTTACAGTTAT--------GTAATTCCTGAAATACAACGGCGGATCTGTGGTATCCTCTGAGCGTAGTAAATTATT--TCTCGCTTTTGTTAGGTGCTGCAGCTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT Pestalotiopsis_versicolor_AF409993_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTATTGCCTTGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCTCTTAGGAGTTGTAGTTCCTAAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTTT-TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCCAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCCCTGAACTT Pestalotiopsis_sinensis_AF409966_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCTCTTCGGAGTTGTAGTTCCTGAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTTT-TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT F003_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCTCTTAGGAGTTGTAGTTCCTGAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTTT-TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCG--------------------------- Pestalotiopsis_sydowiana_HM190154_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCTCTTAGGAGTTGTAGTTCCTGAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTTT-TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT Pestalotiopsis_aquatica_AF409956_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCT-TTA-TAGTTGTAGTTCCTGAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTT--TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGAAATACCCGCTGAACTT Pestalotiopsis_longisetula_AF409971_ GGAGGGATCATTATAGAGTTTTCTAAACTCCCAACCCATGTGAACTTACCTTTTGTTGCCTCGGCAGAAGTT------------------------------------------------------ATAGGTCTTCTTATAGCTGCTGCCGGTGGACCATTAAACTCTTGTTATTTTA-TGTAATCTGAGCGTCTTATTTTAATAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTTCAACCCTTAAGCCTAGCTTAGTGTTGGGAATCTACTTCTTTTATTAGTTGTAGTTCCTGAAATACAACGGCGGATTTGTAGTATCCTCTGAGCGTAGTAA-TTTTTT-TCTCGCTTTTGTTAGGTGCTATAACTCC--CAGCCGCTAAA-CCCCCAA--TTTTTTGTGGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTT ; END; BEGIN TREES; Title PestalotiopsisMB; LINK Taxa = Taxa; TRANSLATE 1 Pestalotiopsis_funerea_OG_EF055197_, 2 Pestalotiopsis_bicilia_OG_AF409973_, 3 F121_, 4 Pestalotiopsis_theae_HQ832793_, 5 Pestalotiopsis_versicolor_AF409993_, 6 Pestalotiopsis_sinensis_AF409966_, 7 F003_, 8 Pestalotiopsis_sydowiana_HM190154_, 9 Pestalotiopsis_aquatica_AF409956_, 10 Pestalotiopsis_longisetula_AF409971_; TREE con_50_majrule = (1:0.00885,2:0.007052,((3:0.003856,4:0.001918)1.00:0.016,((5:0.011692,6:0.003888,7:0.002024,8:0.001959)1.00:0.00695,9:0.003879,10:0.0022)1.00:0.036219)1.00:0.051339); TREE con_50_majrule = (1:0.00885,2:0.007052,((3:0.003856,4:0.001918):0.016,((5:0.011692,6:0.003888,7:0.002024,8:0.001959):0.00695,9:0.003879,10:0.0022):0.036219):0.051339); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 573; END; begin mrbayes; set autoclose = yes nowarn = yes; lset nst = 2 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 - 573; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 573; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1374684524484; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 37662326964161140; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5293590544115717570; mqVersion 275; checksumv 0 3 3534575913 null getNumChars 573 numChars 573 getNumTaxa 10 numTaxa 10 short true bits 15 states 15 sumSquaresStatesOnly 130370.0 sumSquares 130370.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 117; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1006 693; setLocation 82 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #37662326964161140 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #37662326964161140; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 889 626; setLocation 82 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 #37662326964161140 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 865.1306686884406.2852926671647407373; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 889 626; setLocation 82 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 '(1:0.004425,(2:0.007052,((3:0.003856,4:0.001918):0.016,(9:0.003879,10:0.0022,(5:0.011692,6:0.003888,7:0.002024,8:0.001959):0.00695):0.036219):0.051339):0.004425);'; 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 #5293590544115717570 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 889 626; setLocation 82 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;