#NEXUS [written Sun May 04 15:57:48 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 WM114cc211d7328; END; BEGIN TREES; Title 'Trees from "16-epcaLiveSim.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 species_phylogeny = (((1:5.831,(11:8.833[%color = 5 ],(((7:2.0[%color = 16 ],12:1.778[%color = 16 ]):1.857[%color = 16 ],15:1.857[%color = 16 ]):3.2[%color = 16 ],(6:9.0[%color = 13 ],((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):1.6):1.7):1.538,3:8.571[%color = 6 ]):1.857,(13:6.0[%color = 11 ],(((4:4.0[%color = 11 ],10:2.25[%color = 11 ]):2.0[%color = 11 ],9:2.143[%color = 11 ]):2.2[%color = 11 ],2:4.333[%color = 11 ]):4.5[%color = 11 ]):7.5):2.0; TREE symmetrical = ((((1:0.2[%color = 5 ],3:0.2[%color = 5 ]):0.2[%color = 5 ],(6:0.2[%color = 5 ],2:0.2[%color = 5 ]):0.2[%color = 5 ]):0.2[%color = 5 ],((7:0.2[%color = 11 ],12:0.2[%color = 11 ]):0.2[%color = 11 ],(11:0.2[%color = 11 ],15:0.2[%color = 11 ]):0.2[%color = 11 ]):0.2[%color = 11 ]):5.0[%color = 0 ],(((8:0.2[%color = 8 ],14:0.2[%color = 8 ]):0.2[%color = 8 ],(16:0.2[%color = 8 ],5:0.2[%color = 8 ]):0.2[%color = 8 ]):0.2[%color = 8 ],((4:0.2[%color = 6 ],10:0.2[%color = 6 ]):0.2[%color = 6 ],(13:0.2[%color = 6 ],9:0.2[%color = 6 ]):0.2[%color = 6 ]):0.2[%color = 6 ]):5.0):0.2; END; BEGIN NOTES; TEXT FILE TEXT = 'This file shows a "live" EPCA on simulated data of 50 characters, to contrast to a PCA on simulated data. Note that the EPCA doesn''t emphasize the distinctness of major clades nearly as much as does the PCA. To request a new simulated data set, choose "Next source matrix" from the Plot menu of each of the Dependent Tree Windows.^n^nAlso, if you scroll to tree number 2 in the tree window at upper left, you will see characters evolved under a very different tree.^n'; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7000731484956992281 WM114cc211d7328; endTell; getWindow; tell It; setResourcesState false true 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 459 228; setLocation 1 22; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7000731484956992281 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2398.967910429453.8640835773843590908; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 472 341; setLocation 1 362; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; toggleCorners off; 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 off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 26 100 20; setOffsetX 4; setOffsetY 26; setNote Model_tree; setOffsetX 4; setOffsetY 26; endTell; endTell; 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.rhetenor.CharFromOrdinations.CharFromOrdinations; tell It; getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.stochchar.SimulatedMatrix.SimulatedMatrix; tell It; setMatrix 1; setNumChars 50; setCharacterSimulator #mesquite.stochchar.EvolveContinuous.EvolveContinuous; tell It; setModelByName Brownian_default; endTell; setSeed 1; getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 2398.967910429453.8640835773843590908; endTell; endTell; endTell; setOrdinator #mesquite.rhetenor.EvolutionaryPCA.EvolutionaryPCA; tell It; getEmployee #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 2398.967910429453.8640835773843590908; endTell; endTell; 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; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; toggleShowLegend off; setInitialOffsetX -248; setInitialOffsetY -285; setCurrentX 1; setCurrentY 2; show; endTell; setSpotDiameter 10; toggleShowTerminals on; toggleShowInternals on; toggleShowTree on; 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 off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; getWindow; tell It; popAsTile false; popOut; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 467 381; setLocation 978 30; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; newAssistantD #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 56 32; setFont SanSerif; setFontSize 18; setOffsetX 4; setOffsetY 4; setNote EPCA; setOffsetX 4; setOffsetY 4; endTell; endTell; endTell; showWindow; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; endTell; 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.rhetenor.CharFromOrdinations.CharFromOrdinations; tell It; getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.stochchar.SimulatedMatrix.SimulatedMatrix; tell It; setMatrix 1; setNumChars 50; setCharacterSimulator #mesquite.stochchar.EvolveContinuous.EvolveContinuous; tell It; setModelByName Brownian_default; endTell; setSeed 1; getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 2398.967910429453.8640835773843590908; endTell; 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; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; toggleShowLegend off; setInitialOffsetX -218; setInitialOffsetY -288; setCurrentX 1; setCurrentY 2; show; endTell; setSpotDiameter 10; toggleShowTerminals on; toggleShowInternals on; toggleShowTree on; 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 off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; getWindow; tell It; popAsTile false; popOut; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 470 382; setLocation 494 31; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; newAssistantD #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 49 29; setFont SanSerif; setFontSize 18; setOffsetX 4; setOffsetY 4; setNote PCA; setOffsetX 4; setOffsetY 4; endTell; endTell; endTell; showWindow; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; 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; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '17-landmarks.nex'; setPrevFileName '15-epca.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 459 211; setLocation 1 22; setFont SanSerif; setFontSize 10; setActive; setExplanation 'This file shows a "live" EPCA on simulated data of 50 characters, to contrast to a PCA on simulated data. Note that the EPCA doesn''t emphasize the distinctness of major clades nearly as much as does the PCA. To request a new simulated data set, choose "Next Simulated matrix" from the Plot menu of each of the Dependent Tree Windows.^n^nAlso, if you scroll to tree number 2 in the tree window below, you will see characters evolved under a very different tree.^n'; setTitle 'Live sim. - EPCA'; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;