#NEXUS
[written Sat Jun 07 11:23:36 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 WM1148c10e06e14;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "01-coalescence.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 WM1148c10e0900;


END;

BEGIN NOTES;

	TEXT  FILE TEXT = 'This file shows a tree window with gene trees simulated by coalescence within a population.  Scroll through trees to see other simulated gene trees.   The organisms simulated are haploids. The effective population size is by default 10000.  To change this, choose Set Ne from the Tree menu.^n^nTo go to next example file: click the button in the "Go To File" window.^n^nTo duplicate this file: Select "New" from the File menu, and indicate the name of the set of taxa (genes) and the number of taxa (gene copies).  In the list window that will be shown, you may rename the taxa.  Then, select the set of taxa from the "Tree Window" submenu of the Taxa&Trees menu to show a tree window.  Initially, default trees will be shown.  Go to the Tree menu of the tree window, and select "Coalescent trees" from "Simulated Trees" submenu of the the "Tree source" submenu of the "Tree" menu.^n^nTo make it pretty, choose "Curvogram" from the "Tree form" submenu of the Display menu, then choose "Branches Proportional To Lengths" from the Display menu.  To make it so all trees are displayed on the same scale, choose Fixed Scaling and indicate a number about 2-4  times the effective population size. ^n';

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 1469954533384391314 WM1148c10e06e14;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 4636206365576148138 WM1148c10e0900;
			checksum 0 1947097330 WM1148c10e0900;
		endTell;
		getWindow;
		tell It;
			setResourcesState false true 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 452 430;
			setLocation 10 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #1469954533384391314  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.SimulateTree.SimulateTree;
				tell It;
					setTreeSimulator  #mesquite.coalesce.CoalescentTrees.CoalescentTrees;
					tell It;
						getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
						tell It;
							setEffective 10000;
							toggleExponential on;
						endTell;
					endTell;
					setSeed 983242417684;
				endTell;
				setAssignedID 302.971276427933.7117688824995678366;
				getTreeWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 459 407;
					setLocation 490 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					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 30000.0;
						endTell;
						setEdgeWidth 4;
						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;
					setTreeNumber 1;
					useSuggestedSize off;
					toggleSizeToFit on;
					toggleTextOnTree off;
					showWindow;
				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;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '02-coalescence2.nex';
			setPrevFileName '00-introduction.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 452 413;
					setLocation 10 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'This file shows a tree window with gene trees simulated by coalescence within a population.  Scroll through trees to see other simulated gene trees.   The organisms simulated are haploids. The effective population size is by default 10000.  To change this, choose Set Ne from the Coalescent Simulation submenu of the Tree menu.^n^nTo duplicate this file: Select "New" from the File menu, and indicate the name of the set of taxa (genes) and the number of taxa (gene copies).  In the list window that will be shown, you may rename the taxa.  Then, select the set of taxa from the "Tree Window" submenu of the Taxa&Trees menu to show a tree window.  Initially, default trees will be shown.  Go to the Tree menu of the tree window, and select "Coalescent trees" from "Simulated Trees" submenu of the the "Tree Source" submenu of the "Tree" menu.^n^nTo make it pretty, choose "Curvogram" from the "Tree Form" submenu of the Display menu, then choose "Branches Proportional to Lengths" from the Display menu.  To make it so all trees are displayed on the same scale, choose Fixed Scaling and indicate a number about 2-4  times the effective population size. ^n';
				setTitle Simulated_gene_trees;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;