#NEXUS [written Sun Sep 21 19:20:36 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 Matrix_simulated_under_Brownian_motion; DIMENSIONS NCHAR=50; FORMAT DATATYPE = CONTINUOUS; MATRIX taxon_0 -4.387 2.773 -4.485 -6.433 -1.938 10.78 6.534 8.142 7.831 -3.35 2.532 10.64 -1.26 4.666 -9.431 8.031 -2.451 2.829 -7.483 -1.848 -5.781 -3.996 -5.632 0.3009 12.11 -6.342 -1.96 5.876 3.807 5.631 -14.94 -6.966 -3.333 -0.3061 2.18 -4.971 1.885 2.091 -0.0261 8.96 -0.8005 -7.227 -8.465 -7.448 -2.165 2.972 -3.562 -2.488 1.946 -2.334 taxon_1 -1.133 13.72 3.979 3.617 -5.825 -4.591 -6.359 7.814 6.752 -15.24 2.711 -3.876 -5.127 -1.102 15.72 -23.59 7.208 14.19 -14.47 6.917 3.628 16.18 -7.123 11.8 10.16 11.47 -4.599 -2.964 -9.385 -2.568 18.51 4.877 1.605 -6.971 2.89 -0.7017 7.497 5.373 2.523 -15.77 0.29 -0.2348 1.247 2.574 -8.954 11.88 2.504 -0.5636 5.102 16.58 taxon_2 2.46 5.972 0.7667 -12.18 -12.31 9.756 -13.42 1.342 0.4465 -5.557 0.0575 3.818 -11.03 -5.354 11.27 11.77 21.03 0.9194 -0.9012 0.5312 -6.302 0.0443 -0.0528 -4.669 -1.263 -8.891 4.102 -9.944 22.62 1.001 -2.64 13.27 -12.58 -8.012 3.953 2.21 6.804 5.422 13.28 8.453 5.683 -10.22 1.65 -0.5253 -12.71 6.512 8.658 -4.734 0.0085 14.2 taxon_3 -1.11 24.08 -7.304 3.689 -1.192 -15.34 -0.364 1.984 17.34 -7.44 7.164 -7.284 -4.063 -10.2 3.761 -15.98 -0.5717 16.74 -11.32 3.372 4.928 14.97 -2.455 2.873 1.087 11.75 -3.345 6.857 -13.31 0.2848 11.37 8.634 2.322 0.9556 -5.509 2.559 7.726 -3.595 -2.081 -16.37 2.858 4.753 2.017 11.26 -8.238 8.46 5.433 -0.5749 4.876 13.6 taxon_4 -0.719 3.059 -9.676 26.5 -6.016 15.87 -6.141 -1.493 -6.96 1.593 3.401 13.64 3.046 0.5309 7.339 10.73 -5.474 4.652 5.386 -2.431 -8.777 -10.29 -1.347 -10.08 -2.686 12.92 -13.22 -5.268 -3.03 2.877 15.71 0.7509 -1.208 -6.032 5.035 1.372 -8.054 -6.652 -7.332 -0.0727 18.4 17.99 -6.298 -1.446 3.97 4.212 -15.56 -0.5578 12.31 10.52 taxon_5 -5.142 7.274 -2.956 28.68 -3.988 16.34 -7.214 -3.6 -4.003 -9.567 15.3 23.39 21.03 -9.327 10.36 23.82 -4.76 12.5 -3.517 -12.56 -15.86 -13.02 -12.37 -9.585 10.29 21.46 3.047 4.761 11.64 -3.246 7.838 -0.6942 -2.338 -6.366 4.948 18.28 5.103 -20.97 -1.352 4.685 4.125 3.794 -9.578 -2.12 2.91 -12.3 2.121 0.3916 29.41 3.75 taxon_6 0.83 2.284 3.328 -0.7731 -10.05 2.351 4.21 1.643 -5.536 8.155 -11.63 -0.5295 4.39 5.197 -1.236 -0.6901 -1.67 -3.281 7.943 -0.8433 3.624 -2.047 -9.064 -10.4 3.362 4.838 0.1081 1.096 7.444 0.0297 0.5249 0.0115 -11.64 -4.78 3.033 6.569 3.359 -2.734 -2.531 -1.123 -2.026 -0.5421 2.609 -2.765 -0.1815 0.6894 -3.268 -2.307 -1.605 5.747 taxon_7 6.062 -5.615 -12.19 23.56 -11.31 17.66 -9.466 -5.009 -13.21 -1.128 18.43 21.07 -0.7054 1.549 10.54 15.87 -4.521 4.297 -2.267 -0.1179 -4.142 -14.05 12.18 -16.61 6.24 11.15 -0.9985 -7.6 2.902 7.602 25.44 0.5152 0.0578 1.464 -1.108 7.14 -6.992 3.192 -3.92 -1.674 21.81 21.67 -11.06 -8.572 -4.491 10.4 -14.82 8.897 8.738 11.55 taxon_8 0.3838 17.81 -8.098 2.467 -1.112 -14.58 1.561 8.017 16.37 -19.21 2.264 -2.615 -7.028 -6.897 6.483 -14.31 3.535 10.04 -17.79 4.367 4.256 11.1 -6.494 6.95 2.743 11.95 -0.545 1.623 -5.266 -1.137 17.47 2.797 -0.6421 -5.782 -1.228 1.822 6.223 6.345 -0.6809 -14.43 -2.79 5.437 0.1021 8.343 -9.777 7.338 5.844 -0.2151 10.04 8.425 taxon_9 1.615 14.1 -8.764 7.367 -0.4303 -10.12 -7.34 9.748 12.26 -14.35 3.362 -4.01 0.8947 -11.33 2.617 -11.19 4.919 17.18 -15.44 5.075 5.206 13.21 -1.658 0.8625 -0.8543 15.59 2.099 -1.879 -8.221 -4.665 19.02 -2.687 2.739 -1.062 -9.212 5.768 3.105 4.931 -1.515 -14.4 5.562 9.635 -3.785 5.699 -9.886 7.936 5.29 -0.2643 2.489 12.11 taxon_10 -3.728 -2.447 -9.074 -0.9748 7.162 -7.423 6.053 2.913 -0.1297 11.55 -5.164 8.995 -5.174 6.814 -2.894 -7.154 -9.134 -8.277 -0.8106 -6.757 15.67 -23.21 8.179 -7.753 4.521 -24.86 -15.46 12.87 -4.376 -4.549 14.94 10.86 11.83 16.58 1.901 -0.2887 1.363 5.244 2.063 -21.57 9.498 14.29 13.44 -9.728 -0.1529 9.851 -5.584 -8.867 6.659 -0.1165 taxon_11 0.6157 1.165 2.339 -0.696 -9.265 2.158 3.551 -5.069 -4.456 4.274 -11.92 -1.86 7.314 7.502 -2.434 0.4343 -5.92 0.4402 5.258 -2.144 1.232 0.4521 -4.758 -7.469 1.341 6.397 1.426 2.79 4.619 3.767 -0.0603 -2.16 -11.31 -6.574 5.391 10.75 5.083 -1.001 -0.6992 -4.866 -3.299 3.164 3.647 -4.228 0.8009 -0.8905 -5.527 0.1717 -2.532 7.828 taxon_12 -1.439 12.41 1.246 8.377 1.228 -7.186 -2.61 7.866 -2.081 -15.32 4.783 4.182 -14.07 -0.6063 4.706 -18.02 -4.291 4.878 4.116 -5.108 -3.697 7.613 -9.643 2.777 2.016 21.79 2.23 5.665 -8.635 16.69 23.13 7.015 18.85 -0.9347 -4.672 0.3357 5.481 -9.88 -4.331 -15.33 -7.992 1.944 2.395 5.001 -9.506 2.747 -2.986 -7.848 -3.369 12.67 taxon_13 7.512 -0.8567 -8.255 24.63 -5.905 18.8 -13.23 -6.736 -2.307 1.741 15.41 9.391 0.5219 -0.3127 10.27 16.5 -0.9256 3.881 3.214 2.124 -16.67 -15.5 8.06 -14.87 6.52 10.51 -12.57 -3.175 -3.638 4.188 21.89 2.554 -2.49 -1.592 -7.214 8.01 1.808 -10.57 -8.136 -10.06 14.85 11.2 -6.228 -7.617 -1.314 8.792 -14.47 1.924 5.093 4.184 taxon_14 -0.6149 1.497 1.451 -2.767 -9.38 7.198 1.591 3.64 -5.281 7.708 -6.803 -2.367 7.701 9.516 -3.793 1.434 -4.92 -2.344 6.193 0.981 0.9952 -5.392 -6.773 -9.786 1.49 2.854 2.699 1.23 5.97 4.071 0.7833 -1.036 -12.34 -7.296 2.659 10.42 0.1368 -2.094 1.442 1.712 4.475 -0.3893 4.227 -4.588 -7.385 1.038 -5.69 -1.297 -0.2877 8.491 taxon_15 2.506 4.858 -9.529 26.21 -8.406 16.2 -8.264 -1.607 -3.17 6.48 3.535 12.87 2.781 -6.566 13.38 9.009 -2.124 3.319 3.882 -0.5634 -7.139 -9.437 -0.8402 -8.855 1.959 15.79 -13.36 -6.523 -6.204 2.225 18.64 -1.76 0.6178 -5.028 8.987 5.041 -4.244 -3.67 -7.906 -3.457 22.04 16.58 -3.622 -6.66 3.52 2.833 -13.49 -0.5906 14.6 8.093 ; 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 species_phylogeny = (((1:5.83,(11:8.833[%color = 5 ],(((7:2.0,12:1.778):1.857,15:1.857):3.2,(6:9.0[%color = 11 ],((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[%color = 6 ]):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; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 50; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 50; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 662863783909563173; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4091648250786474670; checksum 0 1254086603; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4091648250786474670 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setSize 380 177; setLocation 10 453; 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; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #662863783909563173 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2151.964555237631.1796649727975159086; 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 321 338; setLocation 8 7; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setTreeNumber 1; toggleSizeToFit on; toggleTextOnTree off; 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; makeTreeWindow #662863783909563173 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2169.964555238096.1130981136534120104; 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.rhetenor.CharFromOrdinations.CharFromOrdinations; tell It; getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #4091648250786474670; endTell; endTell; setOrdinator #mesquite.rhetenor.PrincipalComponents.PrincipalComponents; setItem 0; 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 -275; setInitialOffsetY -322; setCurrentX 1; setCurrentY 2; show; endTell; setSpotDiameter 10; 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; getTreeWindow; tell It; setSize 533 342; setLocation 348 22; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; setActive; setTreeNumber 1; toggleSizeToFit on; toggleTextOnTree off; 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 '10-pcaLiveSim.nex'; setPrevFileName '08-anoles.nex'; getWindow; tell It; setSize 439 142; setLocation 429 477; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; setExplanation 'The tree above left was used to simulate evolution by Brownian motion to yield the data matrix shown at left. The same tree is plotted in PCA space calculated from the simulated characters. Notice that the different clades stand out clearly on the plot.^n'; setTitle Simulated_data; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;