#NEXUS [written Sun Sep 21 12:40:34 PDT 2003 by Mesquite version 1.0 (build e57)] BEGIN TAXA; TITLE species; 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 ; END; BEGIN CHARACTERS; TITLE measurements; 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 ; END; BEGIN TREES; Title stored_trees; LINK Taxa = species; 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 = (((1:23.83,(11:8.833,(((7:2.0,12:1.778):1.857,15:1.857):3.2,(6:9.0,((8:4.0,14:3.5):4.0,(16:2.8,5:1.636):3.25):3.0):8.0):1.6):1.7):1.538,3:8.571):1.857,(13:16.0,(((4:4.0,10:2.25):2.0,9:2.143):2.2,2:4.333):2.5):5.5):2.0; END; BEGIN NOTES; TEXT FILE TEXT = 'The tree is drawn here to show branch lengths. (The labels on each node are the reconstructed states.) Because squared-change parsimony uses branch lengths as weights, the reconstruction is sensitive to branch lengths. If you change branch lengths, the reconstruction will change. You can change the branch lengths using the Adjust Branch Length tool (the vertical ruler).^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 1597744227345086770; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5838355485285540067; checksum 0 3542125815; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5838355485285540067 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setSize 457 368; setLocation 7 33; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; toggleShowNames on; toggleTight off; toggleShowChanges on; toggleShowStates on; setColumnWidth 66; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1597744227345086770 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1397.970632252800.6902725252983283785; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setEdgeWidth 8; orientUp; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleCenter on; toggleEven on; namesAngle ?; endTell; endTell; setBackground White; setBranchColor Black; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFont SanSerif; setFontSize 10; setColor Black; toggleColorPartition on; toggleNodeLabels on; toggleShowNames on; endTell; endTell; getTreeWindow; tell It; setSize 722 455; setLocation 218 22; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; toggleSizeToFit off; sizeDrawing 500 400; toggleLegendFloat on; setOrigin 0 0; toggleTextOnTree off; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 65; setOffsetsY 23; getLegendsVector; tell It; distributeCommands; setBounds 285 363 137 37; setOffsetX 65; setOffsetY 23; endDistributeCommands; endTell; newLegendItem #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 #5838355485285540067; endTell; endTell; endTell; endTell; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels on; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters; tell It; setDataSet #5838355485285540067; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; setCharacter 1; toggleShowLegend on; toggleWeights on; setInitialOffsetX -162; setInitialOffsetY -317; setLegendWidth 142; setLegendHeight 302; resume ; endTell; endTell; showWindow; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '05-treeSearch.nex'; setPrevFileName '03-trace.nex'; getWindow; tell It; setSize 519 177; setLocation 10 479; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; setActive; setExplanation 'The tree is drawn here to show branch lengths. (The labels on each node are the reconstructed states.) Because squared-change parsimony uses branch lengths as weights, the reconstruction is sensitive to branch lengths. If you change branch lengths, the reconstruction will change. You can change the branch lengths using the Adjust Branch Length tool (the vertical ruler).^n'; setTitle Branch_lengths; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;