#NEXUS [written Tue Feb 24 18:20:40 PST 2004 by Mesquite version 1.01+ (build e85)] BEGIN TAXA; TITLE flies; DIMENSIONS NTAX=48; TAXLABELS A1 A2 A3 A4 A5 A6 A7 A8 A9 A10 A11 A12 B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 ; END; BEGIN TREES; Title stored_trees; LINK Taxa = flies; TRANSLATE 1 A1, 2 A2, 3 A3, 4 A4, 5 A5, 6 A6, 7 A7, 8 A8, 9 A9, 10 A10, 11 A11, 12 A12, 13 B1, 14 B2, 15 B3, 16 B4, 17 B5, 18 B6, 19 B7, 20 B8, 21 B9, 22 B10, 23 B11, 24 B12, 25 C1, 26 C2, 27 C3, 28 C4, 29 C5, 30 C6, 31 C7, 32 C8, 33 C9, 34 C10, 35 C11, 36 C12, 37 D1, 38 D2, 39 D3, 40 D4, 41 D5, 42 D6, 43 D7, 44 D8, 45 D9, 46 D10, 47 D11, 48 D12; TREE tree = (((((1:2.0,(2:1.0,4:1.0):1.0):2.0,(9:3.0,(10:2.0,(11:1.0,12:1.0):1.0):1.0):1.0):1.0,((3:1.0,6:1.0):2.0,(5:2.0,(7:1.0,8:1.0):1.0):1.0):2.0):2.0[%color = 5 ],((13:1.0,14:1.0):4.0,((((15:1.0,16:1.0):1.0,(18:1.0,19:1.0):1.0):1.0,(17:1.0,22:1.0):2.0):1.0,((20:1.0,21:1.0):1.0,(23:1.0,24:1.0):1.0):2.0):1.0):2.0[%color = 6 ]):3.0,(((25:2.0,(35:1.0,36:1.0):1.0):5.0,(26:6.0,((27:4.0,(29:3.0,(30:2.0,(31:1.0,32:1.0):1.0):1.0):1.0):1.0,(28:2.0,(33:1.0,34:1.0):1.0):3.0):1.0):1.0):2.0[%color = 13 ],(37:7.0,((38:3.0,(46:2.0,(47:1.0,48:1.0):1.0):1.0):3.0,(39:5.0,((40:1.0,44:1.0):3.0,(42:3.0,(41:2.0,(43:1.0,45:1.0):1.0):1.0):1.0):1.0):1.0):1.0):2.0[%color = 11 ]):1.0):0.0; END; BEGIN LABELS; TAXAGROUPLABEL Red COLOR = (RGB 1.0 0.156862753 0.10980392) ; TAXAGROUPLABEL Orange COLOR = (RGB 1.0 0.611764749 0.156862753) ; TAXAGROUPLABEL Cyan COLOR = (RGB 0.286274549 1.0 0.858823551) ; TAXAGROUPLABEL Green COLOR = (RGB 0.211764749 1.0 0.184313751) ; TAXAGROUPLABEL Yellow COLOR = (RGB 0.88235294 1.0 0.172549050) ; TAXAGROUPLABEL Goldenrod; END; BEGIN SETS; TAXPARTITION * UNTITLED = Red : 1 - 12, Orange : 13 - 24, Cyan : 25 - 36, Green : 37 - 48; TAXPARTITION untitled = Red : 1 - 12, Orange : 13 - 24, Cyan : 25 - 36, Green : 37 - 48; TAXPARTITION untitled = Red : 1 - 12, Orange : 13 - 24, Yellow : 25 - 36, Green : 37 - 48; TAXPARTITION species = Red : 1 - 12, Orange : 13 - 24, Yellow : 25 - 36, Goldenrod : 37 - 48; TAXPARTITION untitled = Red : 1 - 12, Orange : 13 - 24, Cyan : 25 - 36, Green : 37 - 48; TAXPARTITION untitled = Red : 1 - 12, Orange : 13 - 24, Yellow : 25 - 36, Green : 37 - 48; TAXPARTITION species = Red : 1 - 12, Orange : 13 - 24, Yellow : 25 - 36, Goldenrod : 37 - 48; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6690059761767473967; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6690059761767473967 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1836.967910171762.6568711385870313008; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setEdgeWidth 4; 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; showNodeNumbers off; labelBranchLengths off; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFont SanSerif; setFontSize 10; setColor Black; toggleColorPartition off; toggleShadePartition on; toggleNodeLabels on; toggleShowNames on; endTell; endTell; getTreeWindow; tell It; setSize 477 392; setLocation 9 13; 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.charts.TaxaScattergram.TaxaScattergram; tell It; setTaxonSource #mesquite.minimal.StoredTaxa.StoredTaxa; tell It; setTaxa #6690059761767473967; endTell; setTaxa #6690059761767473967; axesSame; setValues #mesquite.cont.ContinuousStatesT.ContinuousStatesT; 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 10; setCharacterSimulator #mesquite.stochchar.EvolveContinuous.EvolveContinuous; tell It; setModelByName Brownian_default; endTell; setSeed 995374620870; getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext; tell It; setContextID 1836.967910171762.6568711385870313008; endTell; endTell; endTell; setOrdinator #mesquite.rhetenor.CanonicalVariates.CanonicalVariates; setItem 0; endTell; endTell; setCharacter 2; setItem 0; endTell; showNamesToggle on; getCharter #mesquite.charts.ItemsBiplot.ItemsBiplot; tell It; getWindow; tell It; setX 1; setY 2; setSize 512 452; setLocation 486 9; setFont SanSerif; setFontSize 10; onInfoBar; setExplanationSize 20; setAnnotationSize 20; getToolPalette; tell It; endTell; endTell; enableCalculations; getEmployee #mesquite.charts.Scattergram.Scattergram; tell It; markerSize 10; toggleJoin off; toggleShowDots on; movingWindowSize 1; sumByBlocks off; endTell; endTell; setChartVisible; doCounts; showWindow; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '12-epca.nex'; setPrevFileName '10-pcaLiveSim.nex'; getWindow; tell It; setSize 472 150; setLocation 4 538; setFont SanSerif; setFontSize 10; offInfoBar; setExplanationSize 0; setAnnotationSize 0; setExplanation 'This file shows a Canonical Variates Analysis performed on a data set simulated "live" using Brownian motion evolution on the tree at left. The partition of taxa used to define groups for the CVA represents the four major clades of the tree. By changing the lengths of the colored branches in the tree, the characters simulated will do better or worse at distinguishing the clades via CVA.^n^nTo to ask to resimulate the data, select "Next Simulated matrix" from the "Scattergram" menu.'; setTitle 'Live Simulation -CVA'; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Next; endTell; showWindow; endTell; endTell; end;