#NEXUS
[written Sun May 04 15:08:40 PDT 2008 by Mesquite  version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=9;
	TAXLABELS
		Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa 
	;
	BLOCKID WM11489080c6d26;

END;


BEGIN CHARACTERS;
	TITLE  Structure_&_Color;
	DIMENSIONS  NCHAR=2;
	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "  0 1";
	CHARSTATELABELS 
		1 number_of_eyes /  one two, 2 tail_color /  blue red ; 
	MATRIX
	Aus         11
	Fubonidia   11
	Ibbinidibe  11
	Snorolopa   1(0 1)
	Quidnubia   00
	Suinon      00
	Zorabynyx   00
	Huichoros   00
	Jotinupa    00

;
		BLOCKID WM11489080c980;


END;
BEGIN CHARACTERS;
	TITLE  Measurements;
	DIMENSIONS  NCHAR=4;
	FORMAT DATATYPE = CONTINUOUS;
CHARSTATELABELS 
		1 toe_length,
		2 slime_index,
		3 puncture_density,
		4 sneakiness ; 
	MATRIX
	Aus          0.1217 2.298 0.0 1.0
	Fubonidia    0.111 1.9 1.0 1.0
	Ibbinidibe   0.102 4.2 2.0 0.35
	Snorolopa    0.112 3.7 3.0 0.0
	Quidnubia    0.137 1.3 4.0 0.87
	Suinon       0.145 2.9 5.0 0.05
	Zorabynyx    0.139 2.7 6.0 0.2
	Huichoros    0.108 3.5 7.0 0.0
	Jotinupa     0.156 2.298 8.0 0.0

;
		BLOCKID WM11489080cac0;


END;
BEGIN TREES;
	Title 'Trees from "05-selecting.nex"';
	LINK Taxa = Taxa;
	TRANSLATE
		1 Aus,
		2 Fubonidia,
		3 Ibbinidibe,
		4 Snorolopa,
		5 Quidnubia,
		6 Suinon,
		7 Zorabynyx,
		8 Huichoros,
		9 Jotinupa;
	TREE A_Tree = (((7,6),((9,8),4)),(2,((1,5),3)));

END;


BEGIN NOTES;

	TEXT  TAXA = Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;

	CHARACTERS = Structure_&_Color TAXA = Taxa;
	TEXT   TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red.  Why, no one knows.';

	CHARACTERS = Measurements TAXA = Taxa;

END;

BEGIN LABELS;
	TAXAGROUPLABEL Fubonidiines COLOR = (RGB 0.03137255 0.41176471 1.0) ;
	TAXAGROUPLABEL Jotinupiines COLOR = (RGB 1.0 0.83137255 0.33725490) ;


END;

BEGIN CODONS;
	CODESET * UNTITLED  (CHARACTERS = Structure_&_Color)  =  universal:  1 -  2;


END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE =                                unord PolyTcount =                                MINSTEPS;
	TYPESET * UNTITLED  (CHARACTERS = Structure_&_Color)  =  unord:  1 -  2;
TYPESET Current_Parsimony_Models  (CHARACTERS = Structure_&_Color)  =  unord:  1 -  2;
TYPESET * UNTITLED  (CHARACTERS = Measurements)  =  Squared:  1 -  4;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED  (CHARACTERS = Structure_&_Color)  =  'Mk1 (est.)':  1 -  2;
ProbModelSet * UNTITLED  (CHARACTERS = Measurements)  =  Brownian_default:  1 -  4;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 8476784597994698209 WM11489080c6d26;
			tell It;
				setSelected  4;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 974864624972105434 WM11489080c980;
			checksum 0 4129971366 WM11489080c980;
			setID 1 1065345207404390442 WM11489080cac0;
			checksum 1 2830407910 WM11489080cac0;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 100;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 464;
			setLocation 523 433;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #8476784597994698209  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 535.984012888567.5426059272482531248;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 511 366;
					setLocation 5 401;
					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.DiagonalDrawTree.DiagonalDrawTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							stretchToggle off;
							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;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					useSuggestedSize off;
					toggleSizeToFit on;
					toggleTextOnTree off;
					showWindow;
				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 #1065345207404390442 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 562 329;
					setLocation 461 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;
					setBackground White;
					toggleShowNames on;
					toggleShowTaxonNames on;
					toggleTight off;
					toggleShowChanges on;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames on;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					setColumnWidth 70;
					toggleBirdsEye off;
					toggleAllowAutosize on;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				showWindow;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				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.charts.TaxaScattergram.TaxaScattergram;
		tell It;
			setTaxonSource  #mesquite.minimal.StoredTaxa.StoredTaxa;
			tell It;
				setTaxa #8476784597994698209;
			endTell;
			setTaxa #8476784597994698209;
			axesSame;
			setValues  #mesquite.cont.ContinuousStatesT.ContinuousStatesT;
			tell It;
				getCharacterSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
				tell It;
					setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
					tell It;
						setDataSet #1065345207404390442;
					endTell;
				endTell;
				setCharacter 2;
				setItem 0;
			endTell;
			showNamesToggle on;
			getCharter #mesquite.charts.ItemsBiplot.ItemsBiplot;
			tell It;
				getWindow;
				tell It;
					setX 1;
					setY 2;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 600 407;
					setLocation 523 433;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setActive;
				endTell;
				enableCalculations;
				getEmployee #mesquite.charts.Scattergram.Scattergram;
				tell It;
					markerSize 10;
					toggleJoin off;
					toggleShowDots on;
					movingWindowSize 1;
					sumByBlocks off;
				endTell;
			endTell;
			setChartVisible;
			doCounts;
			showWindow;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '06-selecting.nex';
			setPrevFileName '04-partitions.nex';
			getWindow;
			tell It;
					popAsTile false;
					popOut;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 417 303;
					setLocation 5 24;
					setFont SanSerif;
					setFontSize 10;
				setExplanation 'When taxa are selected in a Character Matrix editor (like that at right), the taxa are not selected merely in that window, but they become selected throughout Mesquite. Note that when this file opens, the taxon Snorolopa is selected in the tree,  matrix and scattergram.^n^nTry selecting a row in the matrix above by touching on the taxon number (to the left of its name); you will see the taxon is selected in the tree window and in the scattergram.^n^nThe Character Matrix Editor and List of Taxa windows share similar methods of selecting taxa.  The selection will accumulate if you hold down the Shift key or the Control key or use a "meta-click" (right mouse button click, or on MacOS command-click).^n^nIf there are magic wands in the tool palette, they will work by selecting those taxa with similar values in the cell touched.  Some of the magic wand tools have drop-down menus to control whether the tool selects taxa with values less than, equal to, and/or greater than that in the cell touched.';
				setTitle Selecting_taxa;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;