#NEXUS [written Fri Feb 20 12:27:15 CET 2009 by Mesquite version 2.01 (build j28) at mac-gibson17-AidanLaptop.local/193.175.249.83] BEGIN TAXA; TITLE vertebrate_genes; DIMENSIONS NTAX=7; TAXLABELS Chick Frog HumanY MouseX RabbitV HumanZ RabbitW ; END; BEGIN TREES; Title RootedGeneTrees; LINK Taxa = vertebrate_genes; TRANSLATE 1 Chick, 2 Frog, 3 HumanY, 4 MouseX, 5 RabbitV, 6 HumanZ, 7 RabbitW; TREE RootedTreeA = ((1:0.2631307650569724,((3:0.15000000000000002,(4:0.05,5:0.05):0.16000000000000003):0.10833333333333334,(6:0.17,7:1.042678362769322):0.05):0.05):0.1985858200838189,2:0.24633591470258132):0.05; TREE RootedTreeB = ((4:0.05,(3:0.15000000000000002,((6:0.17,7:1.042678362769322):0.05,(1:0.2631307650569724,2:0.4449217347864002):0.05):0.10833333333333334):0.16000000000000003):0.025,5:0.025):0.05; TREE RootedTreeC = ((6:0.17,((1:0.2631307650569724,2:0.4449217347864002):0.05,(3:0.15000000000000002,(4:0.05,5:0.05):0.16000000000000003):0.10833333333333334):0.05):0.321339181384661,7:0.721339181384661):0.05; END; BEGIN TAXA; TITLE VertSpeciesTree; DIMENSIONS NTAX=5; TAXLABELS Frog Chick Rabbit Human Mouse ; END; BEGIN TaxaAssociation; TITLE SpeciesGeneAssociations; TAXA VertSpeciesTree , vertebrate_genes; ASSOCIATES Frog / Frog , Chick / Chick , Rabbit / RabbitV RabbitW , Human / HumanY HumanZ , Mouse / MouseX ; END; BEGIN TREES; Title SpeciesTrees; LINK Taxa = VertSpeciesTree; TRANSLATE 1 Frog, 2 Chick, 3 Rabbit, 4 Human, 5 Mouse; TREE SpeciesTree = (1,(2,(4,(3,5)))); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3236621208131690514; setID 1 3640978484080929655; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3236621208131690514 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #3236621208131690514; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 971.1235126592488.8818415304821704619; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 774 524; setLocation 52 54; setFont SanSerif; setFontSize 14; 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 off; toggleBroadScale off; toggleCenter on; toggleEven on; namesAngle ?; endTell; setEdgeWidth 12; orientRight; 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; setFontSize 36; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; endTell; endTell; setTreeNumber 1; useSuggestedSize on; toggleTextOnTree off; endTell; showWindow; 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; endTell; makeTreeWindow #3640978484080929655 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #3640978484080929655; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1047.1235127614848.3931493782365472442; getTreeWindow; tell It; setExplanationSize 70; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 774 484; setLocation 52 54; setFont SanSerif; setFontSize 14; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.assoc.ContainedAssociates.ContainedAssociates; tell It; suppress ; getAssociationSource #mesquite.assoc.StoredAssociations.StoredAssociations; tell It; setCurrentAssociation 0; endTell; getReconstructor #mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory; tell It; toggleUnrooted off; toggleResolve on; toggleUseLengths on; endTell; setEdgeWidth 64; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #3236621208131690514; setTreeBlock 1; toggleUseWeights off; endTell; setContained 3; toggleScale on; setInitialOffsetX -197; setInitialOffsetY -347; desuppress ; getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; namesAngle ?; endTell; endTell; setBackground White; setBranchColor Blue; 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; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; endTell; endTell; setTreeNumber 1; setTree '((2,(4,(5,3))),1);'; useSuggestedSize on; toggleTextOnTree off; endTell; showWindow; 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; endTell; makeTreeWindow #3640978484080929655 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #3640978484080929655; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1077.1235128553586.6467753540364162474; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 774 524; setLocation 52 54; setFont SanSerif; setFontSize 14; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle on; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; namesAngle ?; endTell; setEdgeWidth 12; orientRight; 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; setFontSize 30; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; endTell; endTell; setTreeNumber 1; useSuggestedSize on; toggleTextOnTree off; endTell; showWindow; 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; endTell; endTell; endTell; end;