#NEXUS
[written Sun May 04 15:19:19 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 WM114894f8e2762;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "08-plotTree.nex"';
	DIMENSIONS  NCHAR=5;
	FORMAT DATATYPE = CONTINUOUS;
CHARSTATELABELS 
		1 length,
		2 width,
		3 speed,
		4 temperature,
		5 personality ; 
	MATRIX
	taxon_0    9.367 5.022 2.763 38.57 1.723
	taxon_1    8.793 3.244 4.664 38.81 0.296
	taxon_2    8.576 6.245 2.528 38.5 -0.0239
	taxon_3    11.54 8.718 5.862 40.54 -2.039
	taxon_4    9.977 6.082 5.984 38.32 0.7256
	taxon_5    9.381 5.468 4.398 38.48 1.213
	taxon_6    8.162 5.782 4.894 39.69 0.8212
	taxon_7    8.676 4.86 4.186 39.61 0.5508
	taxon_8    9.356 6.75 4.649 38.01 0.795
	taxon_9    8.107 5.989 2.975 40.13 -1.686
	taxon_10   9.692 7.227 5.747 39.52 -0.8719
	taxon_11   8.902 6.05 4.337 37.5 -0.9571
	taxon_12   9.055 6.575 4.896 40.48 -0.293
	taxon_13   10.11 4.199 3.327 38.94 -0.1349
	taxon_14   10.2 3.975 4.623 37.1 -0.4575
	taxon_15   7.604 5.438 2.809 37.69 -2.129

;
		BLOCKID WM114894f8e530;


END;
BEGIN TREES;
	Title 'Trees from "08-plotTree.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 Phylogeny = (((1:23.83,(11:8.833,(((7:2.0,12:1.778):1.857,15:1.857):3.2,(6:9.0,((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):1.857,(13:16.0,(((4:4.0,10:2.25):2.0,9:2.143):2.2,2:4.333):2.5):5.5):2.0;

END;


BEGIN NOTES;

	TEXT  FILE TEXT = 'The relationships of different characters and phylogeny can be visualized by plotting a tree in a character space.  In the tree window at right, the terminal taxa are placed at their positions in a space of two characters.  The internal nodes are placed at the positions corresponding to their reconstructed ancestral states.  The internal nodes are slightly paler.^n^nBy using the two scrolls you can examine the tree plotted onto other characters.  You can edit the tree to see how ancestral states are reconstructed on different trees.  You might also trace a character (in the Analysis menu) to see three characters at once.';

END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  Squared:  1 -  5;
TYPESET Current_Parsimony_Models   =  Squared:  1 -  5;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  Brownian_default:  1 -  5;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 4132960006106429058 WM114894f8e2762;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 351059586327712100 WM114894f8e530;
			checksum 0 3542125815 WM114894f8e530;
		endTell;
		getWindow;
		tell It;
			setResourcesState false true 100;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 542 300;
			setLocation 7 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #4132960006106429058  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 2152.979145119595.5853167994523254131;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 554 558;
					setLocation 594 52;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					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.charMatrices.StoredCharacters.StoredCharacters;
									tell It;
										setDataSet #351059586327712100;
									endTell;
								endTell;
								setCharacter 2;
								setItem 0;
								getEmployee #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;
							toggleShowLegend on;
							setInitialOffsetX -421;
							setInitialOffsetY -156;
							setCurrentX 1;
							setCurrentY 2;
							show;
						endTell;
						setSpotDiameter 12;
						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;
					setTreeNumber 1;
					useSuggestedSize off;
					toggleSizeToFit on;
					toggleTextOnTree off;
					showWindow;
				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;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #351059586327712100 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 555 228;
					setLocation 16 389;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					colorCells  #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 66;
					toggleBirdsEye off;
					toggleAllowAutosize on;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				showWindow;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				endTell;
				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '09-plotTreeSim.nex';
			setPrevFileName '07-mirrorTree.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 542 283;
					setLocation 7 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'The relationships of different characters and phylogeny can be visualized by plotting a tree in a character space.  In the tree window at right, the terminal taxa are placed at their positions in a space of two characters.  The internal nodes are placed at the positions corresponding to their reconstructed ancestral states.  The internal nodes are slightly paler.^n^nBy using the two scrolls you can examine the tree plotted onto other characters.  You can edit the tree to see how ancestral states are reconstructed on different trees.  You might also trace a character (in the Analysis menu) to see three characters at once.';
				setTitle Plot_tree;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;