#NEXUS
[written Sat Jun 07 11:44:05 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=32;
	TAXLABELS
		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 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32 
	;
	IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
	BLOCKID WM1148f47d2081;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "05-BiSSENetViewer.nex"';
	DIMENSIONS  NCHAR=1;
	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "  0 1";
	MATRIX
	taxon_1   0
	taxon_2   1
	taxon_3   0
	taxon_4   0
	taxon_5   0
	taxon_6   1
	taxon_7   0
	taxon_8   1
	taxon_9   1
	taxon_10  1
	taxon_11  1
	taxon_12  1
	taxon_13  1
	taxon_14  1
	taxon_15  1
	taxon_16  1
	taxon_17  1
	taxon_18  0
	taxon_19  1
	taxon_20  0
	taxon_21  0
	taxon_22  0
	taxon_23  1
	taxon_24  1
	taxon_25  1
	taxon_26  1
	taxon_27  1
	taxon_28  1
	taxon_29  1
	taxon_30  1
	taxon_31  1
	taxon_32  0

;
	IDS WM1148f4828fe0 ;
	BLOCKID WM11493c252d50;


END;
BEGIN TREES;
	Title 'Trees from "05-BiSSENetViewer.nex"';
	LINK Taxa = Untitled_Block_of_Taxa;
	TRANSLATE
		1 taxon_1,
		2 taxon_2,
		3 taxon_3,
		4 taxon_4,
		5 taxon_5,
		6 taxon_6,
		7 taxon_7,
		8 taxon_8,
		9 taxon_9,
		10 taxon_10,
		11 taxon_11,
		12 taxon_12,
		13 taxon_13,
		14 taxon_14,
		15 taxon_15,
		16 taxon_16,
		17 taxon_17,
		18 taxon_18,
		19 taxon_19,
		20 taxon_20,
		21 taxon_21,
		22 taxon_22,
		23 taxon_23,
		24 taxon_24,
		25 taxon_25,
		26 taxon_26,
		27 taxon_27,
		28 taxon_28,
		29 taxon_29,
		30 taxon_30,
		31 taxon_31,
		32 taxon_32;
	TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;

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 6732219986260810463 WM1148f47d2081;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 444104661901299517 WM11493c252d50;
			checksum 0 909469476 WM11493c252d50;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 1213 622;
			setLocation 8 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #6732219986260810463  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 786.1187814845004.4817563795317733133;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1141 555;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
					endTell;
					setActive;
					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 off;
							toggleEven off;
						endTell;
						setEdgeWidth 8;
						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;
					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 #444104661901299517;
							endTell;
						endTell;
						setMethod  #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
						tell It;
							setModelSource  #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
							toggleMPRsMode off;
						endTell;
					endTell;
					setCharacter 1;
					setMapping 1;
					toggleShowLegend on;
					toggleGray off;
					toggleWeights on;
					setInitialOffsetX -362;
					setInitialOffsetY -175;
					setLegendWidth 142;
					setLegendHeight 158;
					resume ;
				endTell;
					newWindowAssistant  #mesquite.diverse.CharAssocDivViewer.CharAssocDivViewer;
				tell It;
					getCharSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
					tell It;
						setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
						tell It;
							setDataSet #444104661901299517;
						endTell;
					endTell;
					setCalculator  #mesquite.diverse.DiversCategCharLikelihood.DiversCategCharLikelihood;
					tell It;
						getIntegTask  #mesquite.diverse.DivCategCharMLCalculator.DivCategCharMLCalculator;
						tell It;
							suspend ;
							setUnderflowCheckFreq 2;
							setStepCount 1000.0;
							setIterations 2;
							conditionOnSurvival  off;
							getStartFromConstrainedModel off;
							resume ;
						endTell;
						setParameters  ?  ?  ?  ?  =2 ?  ?  =4;
					endTell;
					setCharacter -1;
					doCounts;
				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 #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1141 555;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					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 16;
					toggleBirdsEye off;
					toggleAllowAutosize on;
					toggleColorsPanel off;
					toggleDiagonal on;
					setDiagonalHeight 80;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				hideWindow;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				endTell;
				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
				tell It;
					autotabOff;
				endTell;
				getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor;
				tell It;
					panelOpen true;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '06-BiSSEtrees.nex';
			setPrevFileName '04-BiSSEViewer.nex';
			getWindow;
			tell It;
					popAsTile false;
					popOut;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 510 110;
					setLocation 17 725;
					setFont SanSerif;
					setFontSize 10;
				setExplanation 'Here a modified version of BiSSE likelihood calculations is given, which is reparameterized in terms of net diversification (r, speciation minus extinction) and the speciation/extinction ratio (a).';
				setTitle BiSSE_Net_Diversification;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;