#NEXUS [written Sun Sep 21 12:41:02 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 ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 5; TYPESET Current_Parsimony_Models = Squared: 1 - 5; END; BEGIN MESQUITECHARMODELS; CharModel My_Brownian (Brownian) = rate 1.0; ProbModelSet * UNTITLED = Brownian_default: 1 - 5; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7557143514317563732; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6377312818483312110; checksum 0 3542125815; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7557143514317563732 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 4656.968738959275.4595870811122188564; 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 703 426; setLocation 271 2; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; setTree '(((1:5.83,(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,(13:6.0,(((4:4.0,10:2.25):2.0,9:2.143):2.2,2:4.333):4.5):7.5):2.0;'; toggleSizeToFit off; sizeDrawing 500 400; toggleLegendFloat on; setOrigin 0 0; toggleTextOnTree off; newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory; tell It; suspend ; setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree; tell It; toggleLabels off; endTell; setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.stochchar.SimulatedCharacters.SimulatedCharacters; tell It; setSeed 984410176631; setCharacterSimulator #mesquite.stochchar.EvolveContinuous.EvolveContinuous; tell It; setModelByName My_Brownian; endTell; getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 4656.968738959275.4595870811122188564; endTell; endTell; endTell; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; tell It; setDefaultModel 13; endTell; 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 '07-mirrorTree.nex'; setPrevFileName '05-treeSearch.nex'; getWindow; tell It; setSize 377 231; setLocation 18 369; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; setActive; setExplanation 'Characters for tracing and other purposes can come from simulations instead of data matrices. Here, a character is simulated by Brownian motion evolution on the tree. Scroll through other characters. Note that the longer branches tend to show more change.^n^nYou can change branch lengths using the tool that looks like a vertical ruler, or by using the items in the "Branch lengths" submenu of the Tree menu of the tree window. ^n^nYou can change the rate of the evolution by going to the Characters menu and selecting My Brownian under "Edit Character Model". My Brownian is the model of evolution in use in the simulation.^n'; setTitle Simulations; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;