#NEXUS
[written Sat Jun 07 11:31:29 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 WM1148c2e1e9227;

END;



BEGIN TAXA;
	TITLE Genes;
	DIMENSIONS NTAX=5;
	TAXLABELS
		geneA1 geneA2 geneB geneC1 geneC2 
	;
	BLOCKID WM1148c2e1e9628;

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 WM1148c2e1e9227;
			tell It;
				setSelected  3;
				attachments ;
			endTell;
			setID 1 2451688679550742169 WM1148c2e1e9628;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 72;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 583 306;
			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;
					newAssistant  #mesquite.assoc.TaxonListAssoc.TaxonListAssoc;
				tell It;
					getAssociationsTask Stored Taxa Associations (id# 12358);
					resetAssociation;
					getEmployee #mesquite.assoc.StoredAssociations.StoredAssociations;
					tell It;
						setCurrentAssociation 0;
					endTell;
				endTell;
					popAsTile false;
					popOut;
					setExplanationSize 20;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 603 246;
					setLocation 586 405;
					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 536 252;
					setLocation 4 403;
					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 '03-associationsHow3.nex';
			setPrevFileName '02-associationsHow2.nex';
			getWindow;
			tell It;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 511 289;
					setLocation 9 22;
					setFont SanSerif;
					setFontSize 10;
					setActive;
				setExplanation 'The List of Taxa window above for species has a column showing the genes associated with each species, and at right has an editor for the association.  To change what genes are associated with what species, do the following:^n^n1.  select a species^n2. Go to the Associations Editor panel and touch on the genes you want to assign to that species.  Hit the arrow button to assign the genes.^n^nYou can also use the add and subtract buttons to change what genes are assigned to the species.^n^nTo see the next step in analyzing gene trees within species trees, hit the button "Next".';
				setTitle Building_a_Taxa_Association;
				toggleFileNames off;
				setPrevButtonName Previous;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;