#NEXUS
[written Sun May 04 15:07:17 PDT 2008 by Mesquite  version 2.01+ (build j65) at Thrandina.local/10.0.1.8 (Wayne Maddison)]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=9;
	TAXLABELS
		Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa 
	;
	BLOCKID WM11488fd3cf722;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "01-taxa.nex"';
	DIMENSIONS  NCHAR=2;
	FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = "  0 1";
	CHARSTATELABELS 
		1 number_of_eyes /  one two, 2 tail_color /  blue red ; 
	MATRIX
	Aus         11
	Fubonidia   11
	Ibbinidibe  11
	Snorolopa   1(0 1)
	Quidnubia   00
	Suinon      00
	Zorabynyx   00
	Huichoros   00
	Jotinupa    00

;
		BLOCKID WM11488fd3cff0;


END;
BEGIN TREES;
	Title 'Trees from "01-taxa.nex"';
	LINK Taxa = Taxa;
	TRANSLATE
		1 Aus,
		2 Fubonidia,
		3 Ibbinidibe,
		4 Snorolopa,
		5 Quidnubia,
		6 Suinon,
		7 Zorabynyx,
		8 Huichoros,
		9 Jotinupa;
	TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
	TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
	TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
	TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
	TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));

END;


BEGIN NOTES;

	TEXT  TAXA = Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;

	TEXT   TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red.  Why, no one knows.';

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  2;


END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE =                            unord PolyTcount =                            MINSTEPS;
	TYPESET * UNTITLED   =  unord:  1 -  2;
TYPESET Current_Parsimony_Models   =  unord:  1 -  2;

END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  2;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 8476784597994698209 WM11488fd3cf722;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 974864624972105434 WM11488fd3cff0;
			checksum 0 4129971366 WM11488fd3cff0;
		endTell;
		getWindow;
		tell It;
			setResourcesState false false 100;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 968 469;
			setLocation 8 28;
			setFont SanSerif;
			setFontSize 10;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #8476784597994698209 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #8476784597994698209;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 20;
					setAnnotationSize 52;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 468 380;
					setLocation 8 28;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setActive;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
		endTell;
		newAssistant  #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
		tell It;
			setNextFileName '02-addingDeleting.nex';
			setPrevFileName '../introduction.nex';
			getWindow;
			tell It;
					popAsTile true;
					popOut;
					setExplanationSize 0;
					setAnnotationSize 0;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 394 452;
					setLocation 8 28;
					setFont SanSerif;
					setFontSize 10;
				setExplanation 'Taxa (which may represent species or gene sequences) are usually the central entities analyzed by Mesquite.  For instance, character matrices and information about host-parasite associations both relate to taxa. While a block of taxa can exist without a character matrix, a character matrix cannot exist without the taxa to which it refers.  Thus, data files typically have a block of taxa even if they have nothing else.  When you ask Mesquite to create a new file, it asks you about the block of taxa you''d like to put in it.^n^nOnce you have a block of taxa you can see the list of taxa by selecting the List of Taxa menu item (or items from the List of Taxa submenu if there is more than one taxa block) of the Taxa&Trees menu.  At left is a list of taxa.^n^nIn this list of taxa you can rename the taxa by selecting a name using the Edit (I-beam) tool, or by double clicking on the name with the arrow tool.  Type in the new name.  If you hit the "Return" key, Mesquite will move to the next taxon name down.  You can also edit the taxon names in a Character Matrix Editor window.^n^nThis list window also allows you to select taxa, save taxon sets, and view information about the taxa.  It also displays annotations for the taxa (note the asterisk in front of the name "Quidnubia".  Touch on Quidnubia to see the annotation appear in the annotation area at the bottom of the window).^n^nThe project panel at the left lists the block of taxa and the two matrix and trees block connected to it.';
				setTitle Taxa;
				toggleFileNames off;
				setPrevButtonName Return;
				setNextButtonName Next;
			endTell;
			showWindow;
		endTell;
		endTell;
end;