#NEXUS [written Sun Sep 21 12:41:42 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[%color = 6 ],(11:8.833[%color = 10 ],(((7:2.0[%color = 11 ],12:1.778[%color = 11 ]):1.857[%color = 11 ],15:1.857[%color = 11 ]):3.2,(6:9.0[%color = 14 ],((8:4.0[%color = 14 ],14:3.5[%color = 14 ]):4.0[%color = 14 ],(16:2.8[%color = 14 ],5:1.636[%color = 14 ]):3.25[%color = 14 ]):3.0[%color = 14 ]):8.0[%color = 0 ]):1.6):1.7):1.538,3:8.571[%color = 13 ]):1.857,(13:16.0[%color = 5 ],(((4:4.0[%color = 5 ],10:2.25[%color = 5 ]):2.0[%color = 5 ],9:2.143[%color = 5 ]):2.2[%color = 5 ],2:4.333[%color = 5 ]):2.5[%color = 5 ]):5.5):2.0; END; BEGIN NOTES; TEXT FILE TEXT = 'Above left is a tree; above right is the same tree plotted into a space of characters evolving by Brownian motion simulations on the tree itself. The clades are colored to make them distinguishable. Note that the long branches tend to show up as outliers in character space.^n^nYou can scroll from simulated character to character using the blue arrows in the Plot Tree legend.'; 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 1742309196559577302; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8484372108263586382; checksum 0 3542125815; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1742309196559577302 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 464.967909619582.506440536801120907; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.ArcTree.ArcTree; tell It; setEdgeWidth 8; orientRight; 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 423 376; setLocation 7 15; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; toggleSizeToFit on; toggleTextOnTree off; newWindowAssistant #mesquite.trees.DependentTreeWindow.DependentTreeWindow; tell It; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.cont.PlotTree.PlotTree; tell It; setNodeLocs #mesquite.cont.NodeLocs2DPlot.NodeLocs2DPlot; tell It; hide; setAxis #mesquite.cont.MapContinuous.MapContinuous; tell It; getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed; tell It; setCharacterSource #mesquite.stochchar.SimulatedCharacters.SimulatedCharacters; tell It; setSeed 984410506553; setCharacterSimulator #mesquite.stochchar.EvolveContinuous.EvolveContinuous; tell It; setModelByName Brownian_default; endTell; getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 464.967909619582.506440536801120907; endTell; endTell; endTell; setCharacter 2; setItem 0; getEmployee #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; toggleShowLegend on; setInitialOffsetX -387; setInitialOffsetY -156; setCurrentX 1; setCurrentY 2; show; endTell; setSpotDiameter 16; toggleShowInternals on; 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; getWindow; tell It; setSize 510 405; setLocation 453 13; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 0; setAnnotationSize 0; getToolPalette; tell It; endTell; setActive; endTell; showWindow; 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 '../introduction.nex'; setPrevFileName '08-plotTree.nex'; getWindow; tell It; setSize 554 187; setLocation 7 484; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; setExplanation 'Above left is a tree; above right is the same tree plotted into a space of characters evolving by Brownian motion simulations on the tree itself. The clades are colored to make them distinguishable. Note that the long branches tend to show up as outliers in character space.^n^nYou can scroll from simulated character to character using the blue arrows in the Plot Tree legend.'; setTitle Simulations; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Return_to_intro; endTell; showWindow; endTell; endTell; end;