#NEXUS
[written Wed Mar 10 11:51:23 EST 2010 by Mesquite  version 2.72 (build 527) at francois-laptop/127.0.1.1]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=18;
	TAXLABELS
		Myrmecocystuscfnavajo Myrmecocystuscreightoni Myrmecocystusdepilis Myrmecocystuskathjuli Myrmecocystuskennedyi Myrmecocystusmendax Myrmecocystusmexicanus Myrmecocystusmimicus Myrmecocystusnavajo Myrmecocystusnequazcatl Myrmecocystusplacodops Myrmecocystusromainei Myrmecocystussemirufus Myrmecocystussnellingi Myrmecocystustenuinodis Myrmecocystustestaceus Myrmecocystuswheeleri Myrmecocystusyuma 
	;

END;


BEGIN CHARACTERS;
	TITLE  testIncomplete;
	DIMENSIONS  NCHAR=3;
	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "0 1 2";
	CHARSTATELABELS 
		1 Test1 /test1A test1B, 2 Test2 /test2A test2B, 3 Test3 /test3A test3B test3C; 
	MATRIX
	Myrmecocystuscfnavajo    1(0 1)(0 1 2)
	Myrmecocystuscreightoni  ?(0 1)(0 1)
	Myrmecocystusdepilis     102
	Myrmecocystuskathjuli    100
	Myrmecocystuskennedyi    010
	Myrmecocystusmendax      101
	Myrmecocystusmexicanus   000
	Myrmecocystusmimicus     ??0
	Myrmecocystusnavajo      ?11
	Myrmecocystusnequazcatl  100
	Myrmecocystusplacodops   001
	Myrmecocystusromainei    11(0 1 2)
	Myrmecocystussemirufus   001
	Myrmecocystussnellingi   1?0
	Myrmecocystustenuinodis  101
	Myrmecocystustestaceus   ??0
	Myrmecocystuswheeleri    000
	Myrmecocystusyuma        01?

;

END;
BEGIN TREES;
	Title 'Trees from "treepluscharV01.nex"';
	LINK Taxa = Taxa;
	TRANSLATE
		1 Myrmecocystuscfnavajo,
		2 Myrmecocystuscreightoni,
		3 Myrmecocystusdepilis,
		4 Myrmecocystuskathjuli,
		5 Myrmecocystuskennedyi,
		6 Myrmecocystusmendax,
		7 Myrmecocystusmexicanus,
		8 Myrmecocystusmimicus,
		9 Myrmecocystusnavajo,
		10 Myrmecocystusnequazcatl,
		11 Myrmecocystusplacodops,
		12 Myrmecocystusromainei,
		13 Myrmecocystussemirufus,
		14 Myrmecocystussnellingi,
		15 Myrmecocystustenuinodis,
		16 Myrmecocystustestaceus,
		17 Myrmecocystuswheeleri,
		18 Myrmecocystusyuma;
	TREE bestML = (((((((((13:1.724765,11:1.724765):2.926053,6:4.650818):0.689044,(4:1.08387,17:1.08387):4.255993):0.198842,((8:2.708942,3:2.708942):2.027251,((12:2.193845,10:2.193845):2.257581,18:4.451425):0.284767):0.802512):0.506099,5:6.044804):4.524387,2:10.569191):0.836689,(14:2.770378,15:2.770378):8.635503):0.89482,16:12.300701):1.699299,(7:5.724923,(1:2.869547,9:2.869547):2.855375):8.275077);

END;


BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  3;

	EXSET * UNTITLED  =  3;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  3;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1268239884091;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 9015005506118934442;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 2565950173085067248;
			checksumv 0 2 4144740407 null  numChars 3   short true   bits 7   states 7   sumSquaresStatesOnly 220.0   NumFiles 1 NumMatrices 1;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 155;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 1278 934;
			setLocation 1440 0;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #9015005506118934442  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 630.1180487973731.4514395117633566598;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1123 867;
					setLocation 1440 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							inhibitStretchToggle on;
							branchLengthsToggle off;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter off;
							toggleEven off;
						endTell;
						setEdgeWidth 12;
						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;
						toggleShowFootnotes on;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setDrawingSizeMode 0;
					toggleLegendFloat on;
					scale 0;
					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 #2565950173085067248;
							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 4;
					setInitialOffsetY -191;
					setLegendWidth 142;
					setLegendHeight 191;
					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;
					toggleCentred on;
					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 #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1123 867;
					setLocation 1440 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					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;
					toggleThinRows off;
					toggleShowChanges on;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames on;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					setColumnWidth 70;
					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;
			showExtraDataWindow #2565950173085067248 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1123 867;
					setLocation 1440 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
					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;
					toggleThinRows off;
					toggleShowChanges on;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames on;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleAllowAutosize on;
					toggleColorsPanel off;
					toggleDiagonal on;
					setDiagonalHeight 80;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
					getInfoPanel;
					tell It;
						btspOpen true;
						apOpen true;
						fpOpen true;
					endTell;
					toggleInfoPanel off;
				endTell;
				showWindow;
				getWindow;
				tell It;
					forceAutosize;
				endTell;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.categ.StateNamesEditor.StateNamesEditor;
				tell It;
					makeWindow;
					tell It;
						setExplanationSize 30;
						setAnnotationSize 20;
						setFontIncAnnot 0;
						setFontIncExp 0;
						setSize 1123 867;
						setLocation 1440 0;
						setFont SanSerif;
						setFontSize 10;
						getToolPalette;
						tell It;
							setTool mesquite.categ.StateNamesEditor.StateNamesWindow.ibeam;
						endTell;
						setActive;
						rowsAreCharacters on;
						toggleConstrainChar on;
						toggleConstrainCharNum 3;
						togglePanel off;
						toggleSummaryPanel off;
					endTell;
					showWindow;
				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;
		getEmployee  #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			showCharacters #2565950173085067248 #mesquite.lists.CharacterList.CharacterList;
			tell It;
				setData 0;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.DefaultCharOrder.DefaultCharOrder;
					newAssistant  #mesquite.lists.CharListInclusion.CharListInclusion;
					newAssistant  #mesquite.lists.CharListPartition.CharListPartition;
					newAssistant  #mesquite.stochchar.CharListProbModels.CharListProbModels;
					getTable;
					tell It;
						columnWidth 1 101;
					endTell;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1123 867;
					setLocation 1440 0;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.lists.CharacterList.CharacterListWindow.arrow;
					endTell;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.CharListAnnotPanel.CharListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
		endTell;
		endTell;
end;

begin brownie;
taxset all = 1 -18;

END;

