#NEXUS [written Mon Dec 10 11:37:58 JST 2007 by Mesquite version 2.0 (build i71) at tkajig5.local/10.27.1.15] BEGIN TAXA; TITLE Moringaceae_taxa; DIMENSIONS NTAX=14; TAXLABELS Cylicomorpha M.drouhardii M.hildebrandtii M.stenopetala M.ovalifolia M.peregrina M.concanensis M.oleifera M.borziana M.pygmaea M.arborea M.rivae M.ruspoliana M.longituba ; END; BEGIN CHARACTERS; TITLE Stem_Diversity; DIMENSIONS NCHAR=1; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2"; CHARSTATELABELS 1 Stem_Type / Bottle_tree Slender_tree Tuberous_shrub ; MATRIX Cylicomorpha 0 M.drouhardii 0 M.hildebrandtii 0 M.stenopetala 0 M.ovalifolia 0 M.peregrina 1 M.concanensis 1 M.oleifera 1 M.borziana 2 M.pygmaea 2 M.arborea 1 M.rivae 1 M.ruspoliana 1 M.longituba 2 ; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1959356682684768363; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7399029971604539905; checksum 0 253280545 null; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1959356682684768363 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.DefaultTrees.DefaultTrees; setAssignedID 722.1197249239997.1394557659458267827; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1201 683; setLocation 98 179; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.BallsNSticks.BallsNSticks; tell It; setSpotDiameter 22; setEdgeWidth 2; orientRight; useSquare; toggleCosmic off; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; namesAngle ?; endTell; 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; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; endTell; endTell; setTreeNumber 1; setTree '(1:1.0,(2:72.0,(3:28.0,(4:11.0,(5:16.0,((6:6.0,(8:9.0,7:4.0):7.0):46.0,(((9:1.0,10:1.0):8.0,(11:4.0,12:2.0):5.0):4.0,(13:9.0,14:10.0):5.0):44.0):19.0):8.0):9.0):35.0):70.0):0.0;'; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; toggleGray off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #7399029971604539905; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; endTell; endTell; setCharacter 1; setMapping 1; toggleShowLegend on; toggleGray off; toggleWeights on; setInitialOffsetX 20; setInitialOffsetY -401; setLegendWidth 142; setLegendHeight 177; resume ; endTell; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; toggleGray off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #7399029971604539905; endTell; endTell; setMethod #mesquite.stochchar.MargProbAncStates.MargProbAncStates; tell It; setModelSource #mesquite.stochchar.StoredProbModel.StoredProbModel; tell It; setModel 1 'Mk1 (est.)'; endTell; getEmployee #mesquite.stochchar.zMargLikeCateg.zMargLikeCateg; tell It; setReportMode Proportional_Likelihoods; setRootMode Use_Root_State_Frequencies_as_Prior; setDecision 2.0; setUnderflowCheckFreq 2; endTell; endTell; endTell; setCharacter 1; setMapping 1; toggleShowLegend on; toggleGray off; toggleWeights on; setInitialOffsetX 618; setInitialOffsetY -246; setLegendWidth 142; setLegendHeight 177; resume ; endTell; endTell; showWindow; 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; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #7399029971604539905 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1201 683; setLocation 98 179; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 16; toggleBirdsEye off; toggleColorsPanel off; birdsEyeWidth 2; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor; tell It; makeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1201 683; setLocation 98 179; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; rowsAreCharacters on; toggleConstrainChar on; toggleConstrainCharNum 3; togglePanel off; toggleSummaryPanel off; endTell; showWindow; 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.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; endTell; endTell; endTell; end;