#NEXUS
[written Sat Jun 07 11:24:31 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=9;
	TAXLABELS
		g1 g2 g3 g4 g5 g6 g7 g8 g9 
	;
	BLOCKID WM1148c1835ae15;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "02-coalescence2.nex"';
	DIMENSIONS  NCHAR=19;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	g1  AACATCTGGGAACCGTGCG

	g2  C?CGTCTGAGACCCGTCCG

	g3  AAGATACGGGTACCGTCCG

	g4  AACATACGGGAAGCGTCCG

	g5  AAGGTACGGGAACCGTCCG

	g6  AAAGTACGGGACCCGTGCG

	g7  AACGTACGGGAACCGTGCG

	g8  AAAGCACGGGAACCGTGCG

	g9  AACGCACGAGAACCGTGCG


;


		BLOCKID WM1148c1835cf0;


END;

BEGIN NOTES;

	TEXT  FILE TEXT = 'At left is a "Multi Tree Window" to show a series of gene trees simulated by coalescence within a population.  You can scroll down to see other such simulated trees.  Note that the root tends to be between 1000 and 2000 generations deep.^n^nThe effective population size is 1000 (haploid), and can be changed using the "Set Ne.." menu item in the Multi-Tree menu of the Trees window.';

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  19;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  19;
TYPESET Current_Parsimony_Models   =  unord:  1 -  19;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Jukes-Cantor':  1 -  19;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 4451700786596653131 WM1148c1835ae15;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 4972659033594616137 WM1148c1835cf0;
			checksum 0 1947097330 WM1148c1835cf0;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 422 474;
			setLocation 13 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		newAssistant  #mesquite.trees.MultiTreeWindowMaker.MultiTreeWindowMaker;
		tell It;
			setTaxa #4451700786596653131;
			setNumColumns 4;
			setNumRows 4;
			getTreeSource #mesquite.trees.DefiniteTreeSource.DefiniteTreeSource;
			tell It;
				setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
				tell It;
					setTreeSimulator  #mesquite.coalesce.CoalescentTrees.CoalescentTrees;
					tell It;
						getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
						tell It;
							setEffective 1000;
							toggleExponential on;
						endTell;
					endTell;
					setSeed 1189475568974;
				endTell;
				assignNumTrees 100;
			endTell;
			makeWindow;
			toggleLegendBotRight off;
			setNamesVisible on;
			getWindow;
			tell It;
				popAsTile false;
				popOut;
				setExplanationSize 0;
				setAnnotationSize 0;
				setFontIncAnnot 0;
				setFontIncExp 0;
				setSize 626 641;
				setLocation 456 22;
				setFont SanSerif;
				setFontSize 10;
			endTell;
			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 on;
						toggleEven on;
						setFixedScaling 2500.0;
					endTell;
					setEdgeWidth 3;
					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;
					setFont SanSerif;
					setFontSize 10;
					setColor Black;
					toggleColorPartition on;
					toggleShadePartition off;
					toggleNodeLabels on;
					toggleCenterNodeNames off;
					toggleShowNames on;
					namesAngle ?;
				endTell;
			endTell;
			showWindow;
			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;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '03-coalescenceDepth.nex';
			setPrevFileName '01-coalescence.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 350 457;
					setLocation 13 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'At left is a "Multi Tree Window" to show a series of gene trees simulated by coalescence within a population.  You can scroll down to see other such simulated trees.  Note that the root tends to be between 1000 and 2000 generations deep.^n^nThe effective population size is 1000 (haploid), and can be changed using the "Set Ne.." menu item in the Coalescent SImulation submenu of the Multi-Tree menu of the Trees window.';
				setTitle Gene_trees;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;