#NEXUS
[written Sun May 04 15:11:09 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 WM114891f882458;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "04-branchLengths.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 WM114891f88520;


END;
BEGIN TREES;
	Title 'Trees from "04-branchLengths.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 tree is drawn here to show branch lengths.  (The labels on each node are the reconstructed states.) Because squared-change parsimony uses branch lengths as weights, the reconstruction is sensitive to branch lengths.  If you change branch lengths, the reconstruction will change.  You can change the branch lengths using the Adjust Branch Length tool (the vertical ruler).^n';

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;
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			tell It;
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				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1397.970632252800.6902725252983283785;
				getTreeWindow;
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					popAsTile false;
					popOut;
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					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;
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						endTell;
						setEdgeWidth 8;
						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;
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					tell It;
						getEmployee #mesquite.parsimony.TreelengthForMatrix.TreelengthForMatrix;
						tell It;
							getEmployee #mesquite.parsimony.ParsCharSteps.ParsCharSteps;
							tell It;
								setModelSource  #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
								getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
								tell It;
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								endTell;
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								setDataSet #5838355485285540067;
							endTell;
						endTell;
					endTell;
					calculate;
				endTell;
					newAssistant  #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
				tell It;
					suspend ;
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					tell It;
						toggleLabels on;
						toggleGray off;
					endTell;
					setHistorySource  #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
					tell It;
						getCharacterSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
						tell It;
							setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
							tell It;
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							endTell;
						endTell;
						setMethod  #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
						tell It;
							setModelSource  #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
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							getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
							tell It;
								toggleWeight on;
							endTell;
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					setCharacter 1;
					setMapping 1;
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					resume ;
				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;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #5838355485285540067 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					popAsTile false;
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					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
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					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;
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				endTell;
				showWindow;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
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				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 '05-treeSearch.nex';
			setPrevFileName '03-trace.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 485 193;
					setLocation 7 33;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'The tree is drawn here to show branch lengths.  (The labels on each node are the reconstructed states.) Because squared-change parsimony uses branch lengths as weights, the reconstruction is sensitive to branch lengths.  If you change branch lengths, the reconstruction will change.  You can change the branch lengths using the Adjust Branch Length tool (the vertical ruler).^n';
				setTitle Branch_lengths;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;