#NEXUS [written Sat Jun 07 12:31:49 PDT 2008 by Mesquite version 2.5 BETA 2 (build j76) at Thrandina.local/192.168.0.136 (Wayne Maddison)] BEGIN TAXA; TITLE Untitled_Block_of_Taxa; DIMENSIONS NTAX=4; TAXLABELS Box_1 Box_2 Box_3 Box_4 ; BLOCKID WM114cc25684034; END; BEGIN CHARACTERS; TITLE 'Matrix in file "20-landmarks.nex"'; DIMENSIONS NCHAR=4; FORMAT DATATYPE = CONTINUOUS ITEMS = (x y ) GAP = - MISSING = ?; CHARSTATELABELS 3 #4, 4 #3 ; MATRIX Box_1 (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0) Box_2 (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0) Box_3 (0.0 0.0) (0.0 1.0) (0.8 0.8) (1.0 0.0) Box_4 (0.0 0.0) (0.0 1.0) (1.0 1.0) (1.0 0.0) ; BLOCKID WM114cc2568440; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = Squared: 1 - 4; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = Brownian_default: 1 - 4; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5420325524222062819 WM114cc25684034; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4430408865877702767 WM114cc2568440; checksum 0 4234720301 WM114cc2568440; endTell; getWindow; tell It; setResourcesState false true 80; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 520 411; setLocation 3 22; setFont SanSerif; setFontSize 10; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5420325524222062819 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.DefaultTrees.DefaultTrees; setAssignedID 6850.985887405751.627258943310845990; getTreeWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 650 392; setLocation 557 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; stretchToggle off; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter off; toggleEven off; endTell; setEdgeWidth 12; orientUp; 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; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '((1,2),(3,4));'; useSuggestedSize off; toggleSizeToFit on; toggleTextOnTree off; showWindow; newAssistant #mesquite.rhetenor.LandmarkDrawings.LandmarkDrawings; tell It; sizeDrawing 100 60; setInitialOffsetX -204; setInitialOffsetY -146; setItems 0 1; toggleLastToFirst on; getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep; tell It; setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices; tell It; setDataSet #4430408865877702767; endTell; endTell; getReconstructor #mesquite.ancstates.AncestralStatesAll.AncestralStatesAll; tell It; setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates; tell It; setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels; toggleMPRsMode off; getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared; tell It; toggleWeight on; endTell; endTell; endTell; endTell; endTell; desuppressEPCResponse; 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.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4430408865877702767 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; popAsTile false; popOut; setExplanationSize 20; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 633 158; setLocation 560 531; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleShowDefaultCharNames off; toggleConstrainCW on; setColumnWidth 72; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.cont.ItemsEditorForInfoPanel.ItemsEditorForInfoPanel; tell It; panelOpen false; endTell; endTell; endTell; newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator; tell It; setNextFileName '00-introduction.nex'; setPrevFileName '19-landmarks.nex'; getWindow; tell It; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 520 394; setLocation 3 22; setFont SanSerif; setFontSize 10; setActive; setExplanation 'Once the data matrix was entered, we then selected "Landmark Drawings" from the Analysis menu of the Tree window. We chose Stored Matrices.^n^nNote that the most recent common ancestor of Box 3 and Box 4 have the corner somewhat punched in, and the change to Box 3 is indicated by the distortion grid calculated by thin plate splines.^n^nYou''ll notice that some of the points are at the edge of the drawings and not easily visible. The Landmark Drawings module is Mesquite is in its early developmental stages. We''re planning to allow you to show distortions against immediate ancestor, or against the root of the tree.^n^nBy the way, the pictures of fish in the original Landmark example were shown by the Projector module (see the tool in the tool palette). The Projector module can associate pictures to taxa if you hold down the Control key while clicking on a taxon name. It then displays them or turns off display when you use the projector and touch on the taxon name (without Control). '; setTitle 'Landmarks cont''d.'; toggleFileNames off; setPrevButtonName Previous; setNextButtonName Intro.; endTell; showWindow; endTell; endTell; end;