#NEXUS
[written Sat Jun 07 11:24:47 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 WM1148c2865d916;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "03-coalescenceDepth.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 WM1148c2865eb0;


END;

BEGIN NOTES;

	TEXT  FILE TEXT = 'This file contains a small set of taxa representing gene copies within a population.  The chart shows the depth to the last coalescence in a sample of 100 gene trees simulated by coalescence.  ^n^nTo change the number of trees sampled, go to the chart window and select "Number of Trees" from the Chart menu.  The effective population size (haploid) is 1000; change this by choosing "Set Ne" from the Chart window..^n^nTo duplicate this file: Select "New" from the File menu.  Once the file is established, choose "Tree Values" from the Charts menu.  Indicate "Tree Depth" as the value, then "Simulate Trees" as the tree source, "Coalescent trees" as the simulator.  Then, choose "Fixed Number of Groups" under "Grouping on X" and set number to 50.^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 2914423799126459326 WM1148c2865d916;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 5851865005210875165 WM1148c2865eb0;
			checksum 0 1947097330 WM1148c2865eb0;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 442 463;
			setLocation 2 23;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		newAssistant  #mesquite.charts.TreeValuesChart.TreeValuesChart;
		tell It;
			suspendCalculations;
			setTaxa #2914423799126459326;
			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 983242234061;
			endTell;
			setCalculator  #mesquite.coalesce.TreeDepth.TreeDepth;
			getCharter #mesquite.charts.ItemValuesChart.ItemValuesChart;
			tell It;
				getWindow;
				tell It;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 443 426;
					setLocation 472 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					itemsByValues;
					setChartType  #mesquite.charts.Histogram.Histogram;
				tell It;
					suspend;
					showAverageToggle on;
					showPercentToggle off;
					setCumulativeMode 0;
					showAsBarChartToggle on;
					showRawToggle off;
					setNumberIntervals 50;
					setIntervalSize 1.0;
					setMovingWindowSize 5.0 1.0;
					setMode 4;
					resume;
				endTell;
					toggleColorItems off;
					setNumberItems 100;
				endTell;
				enableCalculations;
			endTell;
			setChartVisible;
			doCounts;
			resumeCalculations;
			showWindow;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '04-associations.nex';
			setPrevFileName '02-coalescence2.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 370 446;
					setLocation 2 23;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'This file contains a small set of taxa representing gene copies within a population.  The chart shows the depth to the last coalescence in a sample of 100 gene trees simulated by coalescence.  ^n^nTo change the number of trees sampled, go to the chart window and select "Number of Trees" from the Chart menu.  The effective population size (haploid) is 1000; change this by choosing "Set Ne" from the Coalescent Simulation submenu of the Chart menu of the Chart window.^n^nTo duplicate this file: Select "New" from the file menu.  Once the file is established, choose Analysis>New Bar & Line Chart for>Tree Values.  In the dialog box that appears, check Show Secondary Choices, then select Tree Depth as the value, then "Simulate Trees" as the tree source, "Coalescent trees" as the simulator, and set the effective population size to 1000.  Once the histogram appears, choose "Fixed Number of Groups" in the "Grouping on X" submenu from the Chart menu, and set number to 50.^n';
				setTitle Gene_tree_depths;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;