#NEXUS
[written Sat Jun 07 10:41:06 PDT 2008 by Mesquite  version 2.5 BETA 2 (build j76) at Thrandina.local/192.168.0.136 (Wayne Maddison)]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=10;
	TAXLABELS
		A B C D E F G H I J 
	;
	BLOCKID WM114899ef45e142;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "20-likelihoodToT.nex"';
	DIMENSIONS  NCHAR=1;
	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "  0 1";
	MATRIX
	A  0
	B  0
	C  1
	D  1
	E  1
	F  0
	G  0
	H  0
	I  0
	J  0

;
		BLOCKID WM114899ef46c0;


END;
BEGIN TREES;
	Title 'Trees from "20-likelihoodToT.nex"';
	LINK Taxa = Taxa;
	TRANSLATE
		1 A,
		2 B,
		3 C,
		4 D,
		5 E,
		6 F,
		7 G,
		8 H,
		9 I,
		10 J;
	TREE Tree_1 = (((((1:7.75,(2:6.75,(((5:3.0,3:3.0):0.25,4:3.25):0.5,6:3.75):3.0):1.0):1.0,7:8.75):1.0,10:9.75):1.0,9:10.75):1.0,8:11.75):1.0;
	TREE Tree_2 = (((((1:7.75,(2:6.75,(((5:1.1413990732406842,3:1.1413990732406842):1.684915434733532,4:2.8263145079742165):0.9236854920257835,6:3.75):3.0):1.0):1.0,7:8.75):1.0,10:9.75):1.0,9:10.75):1.0,8:11.75):1.0;
	TREE Tree_3 = (((((1:7.75,(2:6.75,((5:1.1413990732406845,3:1.1413990732406845):2.6086009267593155,(4:1.875,6:1.875):1.875):3.0):1.0):1.0,7:8.75):1.0,10:9.75):1.0,9:10.75):1.0,8:11.75):1.0;
	TREE Tree_4 = (((((1:7.75,(2:6.75,((5:1.1413990732406845,3:1.1413990732406845):2.6086009267593155,6:3.75):3.0):1.0):1.0,(4:4.375,7:4.375):4.375):1.0,10:9.75):1.0,9:10.75):1.0,8:11.75):1.0;

END;


BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 3096529116964699576 WM114899ef45e142;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 5088788982642008211 WM114899ef46c0;
			checksum 0 69473247 WM114899ef46c0;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 576 301;
			setLocation 7 32;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #3096529116964699576  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 500.1054703857709.1750868529321274114;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 543 545;
					setLocation 627 38;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.BallsNSticks.BallsNSticks;
					tell It;
						setSpotDiameter 22;
						setEdgeWidth 2;
						orientRight;
						useDiagonal;
						toggleCosmic off;
						getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle off;
							branchLengthsToggle on;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
						endTell;
					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 18;
						setColor Black;
						toggleColorPartition on;
						toggleShadePartition off;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 2;
					useSuggestedSize off;
					toggleSizeToFit on;
					toggleTextOnTree off;
					showWindow;
					newAssistant  #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
				tell It;
					suspend ;
					setDisplayMode  #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
					tell It;
						toggleLabels off;
						toggleGray off;
					endTell;
					setHistorySource  #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
					tell It;
						getCharacterSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
						tell It;
							setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
							tell It;
								setDataSet #5088788982642008211;
							endTell;
						endTell;
						setMethod  #mesquite.stochchar.MargProbAncStates.MargProbAncStates;
						tell It;
							setModelSource  #mesquite.stochchar.StoredProbModel.StoredProbModel;
							tell It;
								setModel 1   'Mk1 (est.)';
							endTell;
							getEmployee #mesquite.stochchar.zMargLikeCateg.zMargLikeCateg;
							tell It;
								setReportMode Proportional_Likelihoods;
								setRootMode Use_Root_State_Frequencies_as_Prior;
								setDecision 2.0;
								setUnderflowCheckFreq 2;
							endTell;
						endTell;
					endTell;
					setCharacter 1;
					setMapping 1;
					toggleShowLegend on;
					toggleGray off;
					toggleWeights on;
					setInitialOffsetX 3;
					setInitialOffsetY -178;
					setLegendWidth 188;
					setLegendHeight 158;
					resume ;
				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;
			makeTreeWindow #3096529116964699576  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 550.1054705101351.7296501086209055721;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 602 386;
					setLocation 9 414;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.BallsNSticks.BallsNSticks;
					tell It;
						setSpotDiameter 22;
						setEdgeWidth 2;
						orientRight;
						useDiagonal;
						toggleCosmic off;
						getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle on;
							branchLengthsToggle off;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
						endTell;
					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 18;
						setColor Black;
						toggleColorPartition on;
						toggleShadePartition off;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setTree '(((((1:7.75,(2:6.75,((5:1.5,3:3.0):1.5,4:3.25,6:3.75):3.0):1.0):1.0,7:8.75):1.0,10:9.75):1.0,9:10.75):1.0,8:11.75):1.0;';
					useSuggestedSize off;
					toggleSizeToFit on;
					toggleTextOnTree off;
					showWindow;
					newAssistant  #mesquite.ancstates.TraceCharOverTrees.TraceCharOverTrees;
				tell It;
					suppress ;
					setHistorySource  #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
					tell It;
						getCharacterSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
						tell It;
							setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
							tell It;
								setDataSet #5088788982642008211;
							endTell;
						endTell;
						setMethod  #mesquite.stochchar.MargProbAncStates.MargProbAncStates;
						tell It;
							setModelSource  #mesquite.stochchar.CurrentProbModels.CurrentProbModels;
							getEmployee #mesquite.stochchar.zMargLikeCateg.zMargLikeCateg;
							tell It;
								setReportMode Proportional_Likelihoods;
								setRootMode Use_Root_State_Frequencies_as_Prior;
								setDecision 2.0;
								setUnderflowCheckFreq 2;
							endTell;
						endTell;
					endTell;
					setCharacter 1;
					setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
					tell It;
						setTreeBlock 1;
						toggleUseWeights off;
					endTell;
					setNumTrees 100;
					setDisplayMode  #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
					tell It;
						toggleLabels off;
						toggleGray off;
					endTell;
					toggleShowLegend on;
					toggleShowNodeAbsent on;
					toggleShowEquivocal on;
					setMode Count_Trees_with_Uniquely_Best_States;
					setInitialOffsetX 3;
					setInitialOffsetY -368;
					setLegendWidth 142;
					setLegendHeight 190;
					desuppress ;
				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;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '21-likelihoodTot.nex';
			setPrevFileName '19-likelihoodTot.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 504 284;
					setLocation 7 32;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'Below is the same Trace over Trees as in the previous example.  At right is the tree on which there appears to be strong support for state 0 at the MRCA of ECDF.  Why didn''t this get counted in the Trace over Trees?  The reason is that the difference in likelihoods of states 0 and 1 isn''t large enough to be considered "significant".  Hold the cursor over the MRCA of ECDF in the tree at left. The relative likelihoods are 0.81 and 0.19.  However, in the window''s Trace menu, change Report Likelihoods As to "Negative log likelihoods".  These are 5.3 and 6.7.  Pagel (in the manual for Discrete) writes "The conventional cut-off point for preferring one state at a node over the other is if their likelihoods differ by more than 2 log units..."  Trace over Trees uses such a descision threshold, and thus in none of the three trees showing the clade ECDF does the MRCA have an unambiguous reconstruction.   To change the decision threshold, go to the Likelihood Decision Threshold menu item of the Trace_Over_Trees menu.  If you relax it to 1.4, one tree then shows sufficent preference for state 0 that the MRCA of ECDF becomes white in the Trace over Trees.';
				setTitle 'Trace over trees: likelihood';
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;