#NEXUS
[written Sat Jun 07 11:31:22 PDT 2008 by Mesquite  version 2.5 BETA 2 (build j76) at Thrandina.local/192.168.0.136 (Wayne Maddison)]

BEGIN TAXA;
	TITLE Species;
	DIMENSIONS NTAX=3;
	TAXLABELS
		speciesA speciesB speciesC 
	;
	BLOCKID WM1148c2dd53525;

END;



BEGIN TAXA;
	TITLE Genes;
	DIMENSIONS NTAX=5;
	TAXLABELS
		geneA1 geneA2 geneB geneC1 geneC2 
	;
	BLOCKID WM1148c2dd54126;

END;


BEGIN TaxaAssociation;
TITLE how_genes_fit_into_species;
TAXA Species ,  Genes;
ASSOCIATES 

	speciesA /  geneA1 geneA2 , 
	speciesB /  geneB , 
	speciesC /  geneC1 geneC2

;

END;


BEGIN NOTES;

	TEXT  FILE TEXT = 'This file was created as follows.  First, I chose "New" from the File menu.  I indicated the file name in the file dialog box.  Then, when the dialog box came up asking me about a set of taxa, I entered the name ("Species"), and how many taxa (3).  In the taxa list window (e.g., at left), I renamed the taxa (species A, B, C). Next, I made the second set of taxa (e.g., "Genes") by selecting the "New block of taxa" menu item in the Taxa&Trees menu.^n^nNext, I began to indicate how the one set of taxa fits into the other set of taxa.  To do this, I created an "Association" block in the data file (there isn''t a fancy editor for this yet, just a crude one).  I did this by selecting "New Association" in the Taxa&Trees menu.  I was asked to identify the two sets of taxa to be associated, and presented with a simple text editor in a dialog box. ^n^nI then finished writing the "ASSOCIATES" command.  To see an example, go to the Association block window and select "Show example ASSOCIATION block" from the Taxa&Trees menu.  For instance, with these data a possible ASSOCIATES command would be:^n^nASSOCIATES ^n	speciesA /  geneA1 geneA2 , ^n	speciesB /  geneB, ^n	speciesC /  geneC1 geneC2 , ^n;^n^nI entered this.  Then, I closed the Association block window.  This caused the block to be processed.  ^n^nIf you want to see the Association block editor, choose Edit Association from the  Taxa&Trees menu.^n^nTo see the next step in analyzing gene trees within species trees, hit the button in the "Go To File" window.';

END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 2038936534183152982 WM1148c2dd53525;
			setID 1 2451688679550742169 WM1148c2dd54126;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 546 303;
			setLocation 9 22;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #2038936534183152982 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #2038936534183152982;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 550 287;
					setLocation 621 416;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
			showTaxa #2451688679550742169 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #2451688679550742169;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 550 287;
					setLocation 23 411;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '02b-associationsHow2.nex';
			setPrevFileName '01-associationsHow1.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 474 286;
					setLocation 9 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'To indicate what genes belong to what species, you need to define a correspondence between taxa in the two taxa blocks (genes and species).^n^nI created this file as follows.  First, I chose "New" from the File menu.  I indicated the file name in the file dialog box.  Then, when the dialog box came up asking me about a set of taxa, I entered the name ("Species"), and how many taxa (3).  In the taxa list window (e.g., at left), I renamed the taxa (species A, B, C). Next, I made the second set of taxa (e.g., "Genes") by selecting the "New set of taxa" menu item in the Taxa&Trees menu.^n^nNext, I began to indicate how the one set of taxa fits into the other set of taxa.  To do this, I created an "TaxaAssociation" block in the data file.  I did this by selecting "New Association" in the Taxa&Trees menu.  I was asked to identify the two sets of taxa to be associated (usually it''s easier to choose species first), and presented with the List of Taxa window for Species.  ^n^nThe next example file shows how to edit the Taxa Association.';
				setTitle Building_a_Taxa_Association;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;