#NEXUS
[written Sun May 04 15:19:51 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 WM114894fd56a63;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "09-plotTreeSim.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 WM114894fd5950;


END;
BEGIN TREES;
	Title 'Trees from "09-plotTreeSim.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[%color = 6 ],(11:8.833[%color = 10 ],(((7:2.0[%color = 11 ],12:1.778[%color = 11 ]):1.857[%color = 11 ],15:1.857[%color = 11 ]):3.2,(6:9.0[%color = 14 ],((8:4.0[%color = 14 ],14:3.5[%color = 14 ]):4.0[%color = 14 ],(16:2.8[%color = 14 ],5:1.636[%color = 14 ]):3.25[%color = 14 ]):3.0[%color = 14 ]):8.0[%color = 0 ]):1.6):1.7):1.538,3:8.571[%color = 13 ]):1.857,(13:16.0[%color = 5 ],(((4:4.0[%color = 5 ],10:2.25[%color = 5 ]):2.0[%color = 5 ],9:2.143[%color = 5 ]):2.2[%color = 5 ],2:4.333[%color = 5 ]):2.5[%color = 5 ]):5.5):2.0;

END;


BEGIN NOTES;

	TEXT  FILE TEXT = 'Above left is a tree; above right is the same tree plotted into a space of characters evolving by Brownian motion simulations on the tree itself.  The clades are colored to make them distinguishable.  Note that the long branches tend to show up as outliers in character space.^n^nYou can scroll from simulated character to character using the blue arrows in the Plot Tree legend.';

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 1742309196559577302 WM114894fd56a63;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 8484372108263586382 WM114894fd5950;
			checksum 0 3542125815 WM114894fd5950;
		endTell;
		getWindow;
		tell It;
			setResourcesState false true 100;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 524 244;
			setLocation 7 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #1742309196559577302  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 464.967909619582.506440536801120907;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 554 405;
					setLocation 614 39;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.ArcTree.ArcTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle off;
							branchLengthsToggle on;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
						endTell;
						setEdgeWidth 8;
						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;
						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;
					newWindowAssistant  #mesquite.trees.DependentTreeWindow.DependentTreeWindow;
				tell It;
					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.stochchar.SimulatedCharacters.SimulatedCharacters;
										tell It;
											setSeed 984410506553;
											setCharacterSimulator  #mesquite.stochchar.EvolveContinuous.EvolveContinuous;
											tell It;
												setModelByName Brownian_default;
											endTell;
											getTreeSource  #mesquite.trees.TreeOfContext.TreeOfContext;
											tell It;
												setContextID 464.967909619582.506440536801120907;
											endTell;
										endTell;
									endTell;
									setCharacter 2;
									setItem 0;
									getEmployee #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
									tell It;
										setModelSource  #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
										tell It;
											setDefaultModel 13;
										endTell;
										toggleMPRsMode off;
										getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
										tell It;
											toggleWeight on;
										endTell;
									endTell;
								endTell;
								toggleShowLegend on;
								setInitialOffsetX -387;
								setInitialOffsetY -156;
								setCurrentX 1;
								setCurrentY 2;
								show;
							endTell;
							setSpotDiameter 16;
							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;
					getWindow;
					tell It;
						popAsTile false;
						popOut;
						setExplanationSize 0;
						setAnnotationSize 0;
						setFontIncAnnot 0;
						setFontIncExp 0;
						setSize 554 465;
						setLocation 17 345;
						setFont SanSerif;
						setFontSize 10;
						getToolPalette;
						tell It;
						endTell;
					endTell;
					showWindow;
					getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
					tell It;
						colorByPartition off;
					endTell;
				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;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '../introduction.nex';
			setPrevFileName '08-plotTree.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 524 227;
					setLocation 7 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'Here are two windows; one with a tree, and the other with the same tree plotted into a space of characters evolving by Brownian motion simulations on the tree itself.  The clades are colored to make them distinguishable.  Note that the long branches tend to show up as outliers in character space.^n^nYou can scroll from simulated character to character using the blue arrows in the Plot Tree legend.';
				setTitle Simulations;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Return_to_intro;
			endTell;
			showWindow;
		endTell;
		endTell;
end;