#NEXUS
[written Mon Mar 27 11:47:25 EST 2006 by Mesquite  version 1.05 (build g24)]

BEGIN TAXA;
	TITLE empirical_samples;
	DIMENSIONS NTAX=50;
	TAXLABELS
		POP1.1 POP1.3 POP1.5 POP1.8 POP1.10 POP9.2 POP9.3 POP9.6 POP9.8 POP9.9 POP11.1 POP11.2 POP11.6 POP11.8 POP11.10 POP12.2 POP12.3 POP12.6 POP12.8 POP12.9 POP13.2 POP13.4 POP13.5 POP13.7 POP13.11 POP17.1 POP17.3 POP17.5 POP17.7 POP17.10 POP2.2 POP2.5 POP2.6 POP2.7 POP2.10 POP3.1 POP3.2 POP3.4 POP3.7 POP3.8 POP4.4 POP4.5 POP4.7 POP4.8 POP4.10 POP5.2 POP5.5 POP5.6 POP5.7 POP5.9 
	;

END;



BEGIN TAXA;
	TITLE Populations;
	DIMENSIONS NTAX=10;
	TAXLABELS
		POP1E POP9E POP11E POP12E POP13E POP17E POP2W POP3W POP4W POP5W 
	;

END;


BEGIN TaxaAssociation;
TITLE MEMBERSHIP_COI;
TAXA Populations ,  empirical_samples;
ASSOCIATES 

	POP1E /  POP1.1 POP1.3 POP1.5 POP1.8 POP1.10 , 
	POP9E /  POP9.2 POP9.3 POP9.6 POP9.8 POP9.9 , 
	POP11E /  POP11.1 POP11.2 POP11.6 POP11.8 POP11.10 , 
	POP12E /  POP12.2 POP12.3 POP12.6 POP12.8 POP12.9 , 
	POP13E /  POP13.2 POP13.4 POP13.5 POP13.7 POP13.11 , 
	POP17E /  POP17.1 POP17.3 POP17.5 POP17.7 POP17.10 , 
	POP2W /  POP2.2 POP2.5 POP2.6 POP2.7 POP2.10 , 
	POP3W /  POP3.1 POP3.2 POP3.4 POP3.7 POP3.8 , 
	POP4W /  POP4.4 POP4.5 POP4.7 POP4.8 POP4.10 , 
	POP5W /  POP5.2 POP5.5 POP5.6 POP5.7 POP5.9

;

END;


BEGIN MESQUITECHARMODELS;
	CharModel 'COI:base' (StateFrequencyUserSpecifiedDNA) = 
		frequencies = (0.323 0.155 0.15 0.372) ;
	CharModel 'COI:rates' (GammaInvar) = 
		pInvar = 0.7609 shape = 0.884 discrete categories = 4;
	CharModel 'COI:rmat' (RateMatrixGTR) = 
		RMatrix = (1.0 6.26 1.0 1.0 12.78 1.0) ;
	CharModel COI (DNASimulationModel) = 
		'setRootStatesModel ''COI:base''; setEquilStatesModel ''COI:base''; setCharRatesModel ''COI:rates''; setRateMatrixModel ''COI:rmat''; setScalingFactor 1.8E-7; ';
	CharModel 'TrN+I+G_pboot' (DNASimulationModel) = 
		'setRootStatesModel ''COI:base''; setEquilStatesModel ''COI:base''; setCharRatesModel ''COI:rates''; setRateMatrixModel ''COI:rmat''; setScalingFactor 1.0; ';
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 6519456316349128010;
			setID 1 5264020011779768677;
			showTaxa #6519456316349128010 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #6519456316349128010;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setSize 360 400;
					setLocation 367 398;
					setFont SanSerif;
					setFontSize 10;
					onInfoBar;
					setExplanationSize 30;
					setAnnotationSize 20;
					getToolPalette;
					tell It;
					endTell;
					setActive;
				endTell;
				showWindow;
			endTell;
			showTaxa #5264020011779768677 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #5264020011779768677;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setSize 360 400;
					setLocation 5 440;
					setFont SanSerif;
					setFontSize 10;
					onInfoBar;
					setExplanationSize 30;
					setAnnotationSize 20;
					getToolPalette;
					tell It;
					endTell;
				endTell;
				showWindow;
			endTell;
		endTell;
		endTell;
end;