#NEXUS [written Fri Sep 28 19:41:39 CEST 2012 by Mesquite version 2.74 (build 550) at DSK-CROU-012/10.136.102.170] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=20; TAXLABELS Phoma.betae_CBS_109410 Phoma.betae_CBS_523.66_ Ascochyta.hyalospora_CBS_206.80_ Ascochyta.caulina_CBS_344.78_ Ascochyta.caulina_CBS_246.79_ Ascochyta.caulina_CBS_343.78_ Ascochyta.obiones_CBS_786.68 Ascochyta.obiones_CBS_432.77 Coniothyrium.obiones_CBS_453.68_ Phoma.typhina_CBS_132.69_ Phoma.typhina_CBS_602.72_ Phoma.fallens_CBS_161.78_ _Phoma.glaucispora_CBS_284.7 Pleospora.herbarum_CBS_191.86_ Phoma.incompta_CBS_467.76_ _Phoma.incompta_CBS_526.82 Leptosphaeria.clavata_CBS_296.51_ Phoma.flavigena_CBS_314.8_ Phoma.lingam_CBS_147.24_ Phoma.lingam_CBS_260.94_ ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=252; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Phoma.betae_CBS_109410 cggtgacgatgcgccccgtgcagtcttccgtaagtcttgcccccatctcagcgccatc---------------------------------------------------gcgagaagc-ctcttctaacagctctgcagcttccattgtcggccgaccgcgccaccatgggtacgaccctcccct-----agtagctccctcccccgaagt----cccccgaactgaca-agatggcagtatcatgattggt Phoma.betae_CBS_523.66_ cggtgacgatgcgccccgtgcagtcttccgtaagtcttgcccccatctcagcgccatc---------------------------------------------------gcgagaagc-ctcttctgacagctctgcagcttccattgtcggccgaccgcgccaccatgggtacgaccctcccct-----agtagctccctcccccgaagt----cccccgaactgaca-acatggtagtatcatgattggt Ascochyta.hyalospora_CBS_206.80_ cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccattccagcgccatg---------------------------------------------------gcgaccagc-attttctgacggctctgcagcttccattgtcggccgaccgcgccaccacgggtacggccatcccct-----agtagcttcc--ccccaagct----cccccgaactgaca-acatggcagtatcatgattggt Ascochyta.caulina_CBS_344.78_ cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccattccagcgccatg---------------------------------------------------gcgaccagc-attttctgacggctctgcagcttccattgtcggccgaccgcgccaccacgggtacggccatcccct-----agtagcttcc--ccccaagct----cccccgaactgaca-acatggcagtatcatgattggt Ascochyta.caulina_CBS_246.79_ cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccatctcagcgccatc---------------------------------------------------gcgacaagcaattttctgacagctctgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcccct-----agtagcttcc--ccccgagctcctccccccgaactgaca-acatggcagtatcatgattggt Ascochyta.caulina_CBS_343.78_ cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccatctcagcgccatc---------------------------------------------------gcgacaagcaattttctgacagctctgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcccct-----agtagcttcc--ccccgagctcctccccccgaactgaca-acatggcagtatcatgattggt Ascochyta.obiones_CBS_786.68 cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccatctcagcgccatc---------------------------------------------------gcgacaagcaattttctgacagctccgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcccct-----agtagcttcc--ccccgagctcctccccccgaactgaca-acatggcagtatcatgattggt Ascochyta.obiones_CBS_432.77 cggtgacgatgcgccccgtgcagtcttccgtaagtctt---cccatctcagcgccatc---------------------------------------------------gcgacaagcaattttctgacagctccgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcccct-----agtagcttcc--ccccgagct---ccccccgaactgaca-acatggcagtatcatgattggt Coniothyrium.obiones_CBS_453.68_ cggtgacgatgcgccccgagcagtcttccgtaagtcttctccccatgctcgccccgtc---------------------------------------------------gtgaaaacc-gtttcctgacagctccgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcccccc--t-agtagctccc---ccgtgtcccccagacccaaactgaca-gcatggcagtatcatgattggt Phoma.typhina_CBS_132.69_ cggtgatgatgcgccccgagcagtcttccgtaagtactcc-cccattcctgtcttgctggatggaaccacaccaagagcgccattaccggcctccagaaaaggctttttgtgagcatc-cgatgctgacgccctcgcagcttccattgtcggtcggccgcgccaccatgggtatgaaagccctcac----cgcatctcct---gcgtag------tccgcgaactgaca-acatggcagtattatgattggt Phoma.typhina_CBS_602.72_ cggtgatgatgcgccccgagcagtcttccgtaagtactcc-cccattcctgtcttgctggatggaaccacaccaagagcgccattaccggcctccagaaaaggctttttgtgagcatc-cgatgctgacgccctcgcagcttccattgtcggtcggccgcgccaccatgggtatgaaagccctcac----cgcatctcct---gcgtag------tccgcgaactgaca-acatggcagtattatgattggt Phoma.fallens_CBS_161.78_ cggtgacgatgcgccccgagcagtcttccgtaagtacc---tccctgcttgcctcgtccgctgaggccgcatcagaagcgcga------tgcttcggcctctgctgt-ttcttgaacc-aacatctgacaattccgcagcttccattgtcggccgaccgcgccatcatgggtacgatgccctac------agcagctccc---acgcat------tccgcacgctgaca-ccatgatagtattatgatcggt _Phoma.glaucispora_CBS_284.7 cggtgacgatgcgccccgagcagtcttccgtaagtacc---tccctgcttgcctcgtccgctgaggccgcatcagaagcgcca------tacttcggcctctggtgtcttttcgaacc-aacatctgacaattccgcagcttccattgtcggccgaccgcgccatcatgggtacgatgccctac------agcagctccc---acgcat------tccgcgcgctgaca-ccatgatagtattatgatcggt Pleospora.herbarum_CBS_191.86_ cggtgatgatgcgccccgagcagtcttccgtaagtacc---ccagcacccgcctctcgagctggcgctgccccgagagagcga-----------------ccacgccgtgaaagagcc-cgtttctgacagcgctgcagcttccattgtcggccgaccgcgtcaccatgggtacgaccaagctcct----agtaaccctctccgcgtag------cccccaagctgaca-aagcgccagtatcatgattggt Phoma.incompta_CBS_467.76_ cggtgatgatgcgccccgagcagtcttccgtaagtacc---cccattcctgcctcgccagctgaggctgcaccgagagcgcct-----------------ccaggaccgttgagaagc-agcgtctgacagcttcgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcctcctagtgactgactccc---acgtag------tccgcgaactgaca-atatcccagtattatgattggt _Phoma.incompta_CBS_526.82 cggtgatgatgcgccccgagcagtcttccgtaagtacc---cccattcctgcctcgccagctgaggctgcaccgagagcgcct-----------------ccaggaccgttgagaagc-agcgtctgacagcttcgcagcttccattgtcggccgaccgcgccaccatgggtacgaccatcctcctagtgactgactccc---acgtag------tccgcgaactgaca-atatcccagtattatgattggt Leptosphaeria.clavata_CBS_296.51_ cggtgacgatgcgccccgagcagtcttccgtaagtacc---tccatttccgcctc-ccagctgcggcgggatcaaacgccatc--------------------------tcgagag---cacttctgacagctttgcagcttccatcgttggccgaccgcgtcaccatgggtacgatgaaccccc-----cgtagcccct---acgcac------tccgccgtctaaca-aca-aacagtatcatgattggt Phoma.flavigena_CBS_314.8_ cggtgacgatgcgccccgagcagtctttcgtaagtttt---cccgctcatgtcgcgcctcctgcgcccgcaccgagtgcacgc----cttgctttggcctccgatagctgcgaacatc--ctgtctgacaatcctgcagcctccattgtcggccgaccgcgccatcatgggtacgacaatccctca--c-aacagctccc--tccgtga------tctgccagctgaca-acgtggcagtattatgattggt Phoma.lingam_CBS_147.24_ cggtgacgatgcgccccgtgcagtctttcgtaagtctc---cctcca--cgcctccatggacgcgcaggaaacagattttttgcgtgcttctgccggctctagcgca--tcgaaatgt-acatgctaactcaattccagcttccattgtcggccgaccgcgccatcacgggtaggacgatctctcc--ggaccggctatg---acgtgg------cttgtgagctgacagaaaccgcagaatcatgattggt Phoma.lingam_CBS_260.94_ cggtgacgatgcgccccgtgcagtctttcgtaagtctc---cctcca--cgcctccatggacgcgcaggaaacagattttttgcgtgcttctgccggctctagcgca--tcgaaatgt-acatgctaactcaattccagcttccattgtcggccgaccgcgccatcacgggtaggacgatctctcc--ggaccggctatg---acgtgg------cttgtgagctgacagaaaccgcagaatcatgattggt ; END; BEGIN TREES; Title 'Trees from "PleosporaceaeACTc.nex"'; LINK Taxa = Taxa; TRANSLATE 1 Phoma.betae_CBS_109410, 2 Phoma.betae_CBS_523.66_, 3 Ascochyta.hyalospora_CBS_206.80_, 4 Ascochyta.caulina_CBS_344.78_, 5 Ascochyta.caulina_CBS_246.79_, 6 Ascochyta.caulina_CBS_343.78_, 7 Ascochyta.obiones_CBS_786.68, 8 Ascochyta.obiones_CBS_432.77, 9 Coniothyrium.obiones_CBS_453.68_, 10 Phoma.typhina_CBS_132.69_, 11 Phoma.typhina_CBS_602.72_, 12 Phoma.fallens_CBS_161.78_, 13 _Phoma.glaucispora_CBS_284.7, 14 Pleospora.herbarum_CBS_191.86_, 15 Phoma.incompta_CBS_467.76_, 16 _Phoma.incompta_CBS_526.82, 17 Leptosphaeria.clavata_CBS_296.51_, 18 Phoma.flavigena_CBS_314.8_, 19 Phoma.lingam_CBS_147.24_, 20 Phoma.lingam_CBS_260.94_; TREE Figure_4 = (20:0.005161,19:0.006069,(((((1:0.020023,2:0.012274)0.99:0.050539,(3:0.007022,4:0.006561)1.00:0.05976,5:0.00632,6:0.006317,(7:0.006885,8:0.007278)0.70:0.011305)0.99:0.131823,9:0.100123)0.52:0.049934,(((10:0.00513,11:0.005422)1.00:0.332964,(14:0.278387,(15:0.005176,16:0.005692)0.99:0.07276)0.69:0.048428)0.52:0.044234,((12:0.025519,13:0.014575)1.00:0.205553,17:0.243903)0.79:0.071183)0.88:0.097354)0.75:0.136797,18:0.207573)1.00:0.735168); END; begin MrBayes; log start filename = PleosporaaceaeACT.log; outgroup CBS260.94Phoma.lingam; lset nst = 2 rates = gamma; mcmc temp = 0.05 ngen = 5000000 samplefreq = 10 stoprule = yes; plot; sump; sumt; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 252; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 252; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 252; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1348854099266; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3826610407295060282; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7320229111549607890; mqVersion 274; checksumv 0 2 716036101 null getNumChars 252 numChars 252 getNumTaxa 20 numTaxa 20 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 81342.0 sumSquares -7.286463909115273E20 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 242; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1920 972; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3826610407295060282 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3826610407295060282; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1678 905; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; 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.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1678 905; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3826610407295060282 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1515.1348854060163.1467130687816352428; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1678 905; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 6; orientUp; 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; 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; 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 #7320229111549607890 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1678 905; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;