#NEXUS
[written Sun May 04 15:26:24 PDT 2008 by Mesquite  version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=48;
	TAXLABELS
		nig1 nig2 nig3 nig4 nig5 nig6 nig7 nig8 nig9 nig10 nig11 nig12 met1 met2 met3 met4 met5 met6 met7 met8 met9 met10 met11 met12 moj1 moj2 moj3 moj4 moj5 moj6 moj7 moj8 moj9 moj10 moj11 moj12 pac1 pac2 pac3 pac4 pac5 pac6 pac7 pac8 pac9 pac10 pac11 pac12 
	;
	BLOCKID WM114cbd5b9f97;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "03-wingsCVA.nex"';
	DIMENSIONS  NCHAR=4;
	FORMAT DATATYPE = CONTINUOUS;
CHARSTATELABELS 
		1 V1,
		2 V2,
		3 ACV,
		4 PCV ; 
	MATRIX
	nig1    1.784 1.994 0.1007 0.2488
	nig2    1.662 1.946 0.0882 0.2503
	nig3    1.92 2.244 0.0678 0.2707
	nig4    1.838 2.107 0.0678 0.2653
	nig5    1.843 2.111 0.0784 0.2791
	nig6    1.953 2.194 0.0671 0.2696
	nig7    1.782 2.03 0.0795 0.2678
	nig8    1.792 2.137 0.0852 0.2694
	nig9    1.889 2.203 0.0746 0.2575
	nig10   1.836 2.092 0.0925 0.2592
	nig11   1.877 2.13 0.0941 0.2696
	nig12   1.826 2.133 0.0741 0.2751
	met1    1.451 1.659 0.0805 0.2425
	met2    1.672 1.949 0.0754 0.2687
	met3    1.67 1.943 0.0745 0.2862
	met4    1.783 2.037 0.1074 0.2612
	met5    1.734 2.048 0.0814 0.2503
	met6    1.624 1.858 0.0736 0.2555
	met7    1.697 1.939 0.0871 0.2728
	met8    1.695 1.979 0.0923 0.2748
	met9    1.552 1.835 0.0674 0.2417
	met10   1.7 1.994 0.0875 0.2781
	met11   1.723 1.945 0.0808 0.2705
	met12   1.688 1.987 0.0875 0.2847
	moj1    1.19 1.298 0.0667 0.1871
	moj2    1.209 1.336 0.06 0.1962
	moj3    1.255 1.387 0.0806 0.2011
	moj4    1.224 1.351 0.0666 0.1847
	moj5    1.196 1.318 0.0596 0.176
	moj6    1.188 1.345 0.074 0.1991
	moj7    1.187 1.314 0.0696 0.1745
	moj8    1.235 1.371 0.06 0.1877
	moj9    1.153 1.29 0.0471 0.1688
	moj10   1.208 1.352 0.0731 0.1818
	moj11   1.177 1.29 0.0679 0.1777
	moj12   1.226 1.363 0.06 0.1909
	pac1    1.343 1.479 0.0821 0.1719
	pac2    1.429 1.56 0.0731 0.2052
	pac3    1.391 1.537 0.0731 0.2192
	pac4    1.496 1.673 0.093 0.2283
	pac5    1.347 1.514 0.0795 0.1978
	pac6    1.311 1.449 0.062 0.1795
	pac7    1.424 1.62 0.0682 0.21
	pac8    1.411 1.596 0.0787 0.2128
	pac9    1.338 1.502 0.0653 0.2077
	pac10   1.449 1.618 0.0745 0.231
	pac11   1.447 1.603 0.0787 0.2346
	pac12   1.465 1.621 0.0765 0.214

;
		BLOCKID WM114cbd5ba370;


END;
BEGIN TREES;
	Title 'Trees from "03-wingsCVA.nex"';
	LINK Taxa = Taxa;
	TRANSLATE
		1 nig1,
		2 nig2,
		3 nig3,
		4 nig4,
		5 nig5,
		6 nig6,
		7 nig7,
		8 nig8,
		9 nig9,
		10 nig10,
		11 nig11,
		12 nig12,
		13 met1,
		14 met2,
		15 met3,
		16 met4,
		17 met5,
		18 met6,
		19 met7,
		20 met8,
		21 met9,
		22 met10,
		23 met11,
		24 met12,
		25 moj1,
		26 moj2,
		27 moj3,
		28 moj4,
		29 moj5,
		30 moj6,
		31 moj7,
		32 moj8,
		33 moj9,
		34 moj10,
		35 moj11,
		36 moj12,
		37 pac1,
		38 pac2,
		39 pac3,
		40 pac4,
		41 pac5,
		42 pac6,
		43 pac7,
		44 pac8,
		45 pac9,
		46 pac10,
		47 pac11,
		48 pac12;
	TREE colored = (((1[%color = 5 ],(2[%color = 5 ],(3[%color = 5 ],(4[%color = 5 ],(5[%color = 5 ],(6[%color = 5 ],(7[%color = 5 ],(8[%color = 5 ],(9[%color = 5 ],(10[%color = 5 ],(11[%color = 5 ],12[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ])[%color = 5 ],(13[%color = 8 ],(14[%color = 8 ],(15[%color = 8 ],(16[%color = 8 ],(17[%color = 8 ],(18[%color = 8 ],(19[%color = 8 ],(20[%color = 8 ],(21[%color = 8 ],(22[%color = 8 ],(23[%color = 8 ],24[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ])[%color = 8 ]),((25[%color = 10 ],(26[%color = 10 ],(27[%color = 10 ],(28[%color = 10 ],(29[%color = 10 ],(30[%color = 10 ],(31[%color = 10 ],(32[%color = 10 ],(33[%color = 10 ],(34[%color = 10 ],(35[%color = 10 ],36[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ])[%color = 10 ],(37[%color = 11 ],(38[%color = 11 ],(39[%color = 11 ],(40[%color = 11 ],(42[%color = 11 ],(41[%color = 11 ],(43[%color = 11 ],(44[%color = 11 ],(45[%color = 11 ],(46[%color = 11 ],(47[%color = 11 ],48[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ])[%color = 11 ]));

END;


BEGIN LABELS;
	TAXAGROUPLABEL nig COLOR = (RGB 1.0 0.03137255 0.25882353) ;
	TAXAGROUPLABEL met COLOR = (RGB 0.25882353 1.0 0.08627451) ;
	TAXAGROUPLABEL moj COLOR = (RGB 1.0 0.62745098 0.05882353) ;
	TAXAGROUPLABEL pac COLOR = (RGB 0.02745098 0.58431373 1.0) ;


END;

BEGIN SETS;
	TAXPARTITION * UNTITLED  =  nig :  1 -  12, met :  13 -  24, moj :  25 -  36, pac :  37 -  48;
	TAXPARTITION species  =  nig :  1 -  12, met :  13 -  24, moj :  25 -  36, pac :  37 -  48;

END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  Squared:  1 -  4;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  Brownian_default:  1 -  4;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 5510618219447170949 WM114cbd5b9f97;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 3229888185240561153 WM114cbd5ba370;
			checksum 0 578547273 WM114cbd5ba370;
		endTell;
		getWindow;
		tell It;
			setResourcesState false true 100;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 478 203;
			setLocation 12 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #3229888185240561153 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 478 146;
					setLocation 12 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 #5510618219447170949;
			endTell;
			setTaxa #5510618219447170949;
			axesSame;
			setValues  #mesquite.cont.ContinuousStatesT.ContinuousStatesT;
			tell It;
				getCharacterSource  #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
				tell It;
					setCharacterSource #mesquite.rhetenor.CharFromOrdinations.CharFromOrdinations;
					tell It;
						getCharacterSource #mesquite.charMatrices.CharMatrixCoordIndep.CharMatrixCoordIndep;
						tell It;
							setCharacterSource #mesquite.charMatrices.StoredMatrices.StoredMatrices;
							tell It;
								setDataSet #3229888185240561153;
							endTell;
						endTell;
						setOrdinator #mesquite.rhetenor.CanonicalVariates.CanonicalVariates;
						setItem 0;
						hireAssistant  #mesquite.rhetenor.ShowCharLoadings.ShowCharLoadings;
						tell It;
							getCharter #mesquite.charts.ItemValuesChart.ItemValuesChart;
							tell It;
								getWindow;
								tell It;
									popAsTile false;
									popOut;
									setExplanationSize 20;
									setAnnotationSize 20;
									setFontIncAnnot 0;
									setFontIncExp 0;
									setSize 492 463;
									setLocation 8 322;
									setFont SanSerif;
									setFontSize 10;
									getToolPalette;
									tell It;
									endTell;
									valuesByItems;
									setChartType  #mesquite.charts.Histogram.Histogram;
								tell It;
									suspend;
									showAverageToggle on;
									showPercentToggle off;
									setCumulativeMode 0;
									showAsBarChartToggle on;
									showRawToggle off;
									setNumberIntervals 20;
									setIntervalSize 1.0;
									setMovingWindowSize 5.0 1.0;
									setMode 0;
									resume;
								endTell;
									toggleColorItems off;
									setNumberItems 4;
								endTell;
								enableCalculations;
							endTell;
							setChartVisible;
							doCounts;
							showWindow;
						endTell;
					endTell;
				endTell;
				setCharacter 2;
				setItem 0;
			endTell;
			showNamesToggle on;
			getCharter #mesquite.charts.ItemsBiplot.ItemsBiplot;
			tell It;
				getWindow;
				tell It;
					setX 1;
					setY 2;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 518 433;
					setLocation 538 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
				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 '04-anoles.nex';
			setPrevFileName '02-wingsPCA.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 478 186;
					setLocation 12 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'In the scatter plot, a Canonical Variates Analysis is shown, which uses the partition into the four species as the a priori grouping.  The bar chart shows the character loadings on each of the canonical variates.  Note that character 1 loads most highly on the first variate.';
				setTitle Canonical_Variates;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;