#NEXUS [written Sun May 04 15:10:53 PDT 2008 by Mesquite version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS taxon_0 taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 ; BLOCKID WM114891f200a57; END; BEGIN CHARACTERS; TITLE 'Matrix in file "03-trace.nex"'; DIMENSIONS NCHAR=5; FORMAT DATATYPE = CONTINUOUS; CHARSTATELABELS 1 length, 2 width, 3 speed, 4 temperature, 5 personality ; MATRIX taxon_0 9.367 5.022 2.763 38.57 1.723 taxon_1 8.793 3.244 4.664 38.81 0.296 taxon_2 8.576 6.245 2.528 38.5 -0.0239 taxon_3 11.54 8.718 5.862 40.54 -2.039 taxon_4 9.977 6.082 5.984 38.32 0.7256 taxon_5 9.381 5.468 4.398 38.48 1.213 taxon_6 8.162 5.782 4.894 39.69 0.8212 taxon_7 8.676 4.86 4.186 39.61 0.5508 taxon_8 9.356 6.75 4.649 38.01 0.795 taxon_9 8.107 5.989 2.975 40.13 -1.686 taxon_10 9.692 7.227 5.747 39.52 -0.8719 taxon_11 8.902 6.05 4.337 37.5 -0.9571 taxon_12 9.055 6.575 4.896 40.48 -0.293 taxon_13 10.11 4.199 3.327 38.94 -0.1349 taxon_14 10.2 3.975 4.623 37.1 -0.4575 taxon_15 7.604 5.438 2.809 37.69 -2.129 ; BLOCKID WM114891f20190; END; BEGIN TREES; Title 'Trees from "03-trace.nex"'; LINK Taxa = Taxa; TRANSLATE 1 taxon_0, 2 taxon_1, 3 taxon_2, 4 taxon_3, 5 taxon_4, 6 taxon_5, 7 taxon_6, 8 taxon_7, 9 taxon_8, 10 taxon_9, 11 taxon_10, 12 taxon_11, 13 taxon_12, 14 taxon_13, 15 taxon_14, 16 taxon_15; TREE Phylogeny = (((1:6.0,(11:5.0,(((7:1.0,12:1.0):1.0,15:2.0):2.0,(6:3.0,((8:1.0,14:1.0):1.0,(16:1.0,5:1.0):1.0):1.0):1.0):1.0):1.0):1.0,3:7.0):1.0,(13:4.0,(((4:1.0,10:1.0):1.0,9:2.0):1.0,2:3.0):1.0):4.0):1.0; END; BEGIN NOTES; TEXT FILE TEXT = 'This file shows a tree window in which you can edit and analyze trees. The evolution of a character is reconstructed and traced using squared change parsimony. There is also a legend showing the treelength summed over the characters in the matrix.^n^nUse the tools to edit the tree. Note that the reconstruction and treelength are updated. Also, edit the data matrix. The reconstruction and treelength are updated as you make changes.^n'; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 5; TYPESET Current_Parsimony_Models = Squared: 1 - 5; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 5; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5221598931228393166 WM114891f200a57; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2482145747186088434 WM114891f20190; checksum 0 3542125815 WM114891f20190; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 610 294; setLocation 7 33; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5221598931228393166 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 533.967563158321.34715281069351178; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 585 442; setLocation 633 34; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; endTell; setEdgeWidth 12; 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; setFont SanSerif; setFontSize 10; setColor Black; toggleColorPartition on; toggleShadePartition on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 13; setOffsetsY 295; getLegendsVector; tell It; distributeCommands; setBounds 13 295 137 39; setOffsetX 13; setOffsetY 295; endDistributeCommands; endTell; newLegendItemNoCalc #mesquite.parsimony.Treelength.Treelength; tell It; getEmployee #mesquite.parsimony.TreelengthForMatrix.TreelengthForMatrix; tell It; getEmployee #mesquite.parsimony.ParsCharSteps.ParsCharSteps; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #2482145747186088434; endTell; endTell; endTell; calculate; 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 #2482145747186088434; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; setCharacter 1; setMapping 1; toggleShowLegend on; toggleGray off; toggleWeights on; setInitialOffsetX -162; setInitialOffsetY -307; setLegendWidth 142; setLegendHeight 305; resume ; endTell; endTell; 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.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #2482145747186088434 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 581 387; setLocation 10 370; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 66; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; 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; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '04-branchLengths.nex'; setPrevFileName '01-editContinuous.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 610 277; setLocation 7 33; setFont SanSerif; setFontSize 10; setActive; setExplanation 'This file shows a tree window in which you can edit and analyze trees. The evolution of a character is reconstructed and traced using squared change parsimony. There is also a legend showing the treelength summed over the characters in the matrix.^n^nUse the tools to edit the tree. Note that the reconstruction and treelength are updated. Also, edit the data matrix. The reconstruction and treelength are updated as you make changes.^n'; setTitle Ancestral_states; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;