#NEXUS
[written Wed Oct 01 09:44:58 EDT 2014 by Mesquite  version 3.01 (build 658) at naama-mendas-macbook-4.local/192.168.1.146]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=7;
	TAXLABELS
		Solanum_lycopersicum_Heinz1706 Solanum_lycopersicum_YP Solanum_lycopersicum_GH13 Solanum_pimpinellifolium_LA1589 Solanum_galapagense_LA0436 Solanum_lycopersicum_BTI87 Solanum_chilense_LA2779 
	;

END;


BEGIN TREES;
	Title Imported_trees;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 Solanum_lycopersicum_Heinz1706,
[1] 		2 Solanum_lycopersicum_YP,
[2] 		3 Solanum_lycopersicum_GH13,
[3] 		4 Solanum_pimpinellifolium_LA1589,
[4] 		5 Solanum_galapagense_LA0436,
[5] 		6 Solanum_lycopersicum_BTI87,
[6] 		7 Solanum_chilense_LA2779;
	TREE Imported_tree_1 = ((((((1,2)0.67,(3,4)0.89)0.27,(5))0.25,6),7));

END;



BEGIN TAXA;
	TITLE Taxa2;
	DIMENSIONS NTAX=7;
	TAXLABELS
		Solanum_lycopersicum_Heinz1706 Solanum_lycopersicum_YP Solanum_lycopersicum_GH13 Solanum_lycopersicum_BTI87 Solanum_galapagense_LA0436 Solanum_pimpinellifolium_LA1589 Solanum_chilense_LA2779 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	LINK TAXA = Taxa2;
	DIMENSIONS  NCHAR=274;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	Solanum_lycopersicum_Heinz1706   GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGAAATATTTAGTATCGGCAAACCGATGTGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGCTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_lycopersicum_YP          GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGAAATATTTAGTATCGGCAAACCGATGTGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGCTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_lycopersicum_GH13        GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGCAATATTTAGTATCGGCAAACCGATGCGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGTTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_lycopersicum_BTI87       GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGCAATATTTAGTATCGGCAAACCGATGTGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGCTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_galapagense_LA0436       GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGCAATATTTAGTATCGGCAAACCGATGTGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGCTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_pimpinellifolium_LA1589  GCCTTGGCTTATTGGGCCTGCCATTGGCAAAAATATTTAGAGTGATGTGCGCCTGTTACGAACGATGCTAATAGGCAATATTTAGTATCGGCAAACCGATGCGTGTAAGCTACGGAAGCTGATGGTAGGCAATGATTGACGTCGGTAGAGGGATGTGTGCAAGATATAGACGATGTTGTCAGACCATGTTTTACATCAAGAAACTGATGTGTTAAGGTTGCGGGCGATGATGGAAGCCCAGGTTGGTCGTCGGCAGACCCTTGTGTGCATCC--
	Solanum_chilense_LA2779          -----------------------------AAAATCTTCAGAGTGATGTGTGCCTGTTACGAACGATGCTAATAGGCCATATTCAGTGTCGGCAAACCGATGTGTGTAGACTACA?AAGCTGATGGTAGGCAAAATTTGACGTCAGAAGAGGGATGTGTGCAAGATATAGACGATGCTGTCAGACCATGTTTTACATCAAGAAGCTGATGTCTGAAGGCTGCGGGC?ATGATGGCAGCCCAAGTTGGACGCCAGCAGACCCTTGTGTGCATCC--

;



END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  274;

END;

BEGIN NOTES;

	TAXABITS   TAXA = Taxa2 NAME = newlyAddedTaxon on =  1 -  7;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  274;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Jukes-Cantor':  1 -  274;
END;

Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1412171099094;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 7999089955036732026;
			setID 1 8974278400501739039;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 3954759578666495103;
			mqVersion 301;
			checksumv 0 3 2471879655 null  getNumChars 274 numChars 274 getNumTaxa 7 numTaxa 7   short true   bits 15   states 15   sumSquaresStatesOnly 42520.0 sumSquares 42520.0 longCompressibleToShort false usingShortMatrix true   NumFiles 1 NumMatrices 1 errorReportedDuringRun;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 191;
			setPopoutState 400;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 472;
			setLocation 8 22;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #7999089955036732026 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #7999089955036732026;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 509 400;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam;
					endTell;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.ColorTaxon.ColorTaxon;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
			showTaxa #8974278400501739039 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #8974278400501739039;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 509 400;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam;
					endTell;
					setActive;
				endTell;
				showWindow;
				getEmployee #mesquite.lists.ColorTaxon.ColorTaxon;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
				tell It;
					togglePanel off;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #7999089955036732026  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTaxa #7999089955036732026;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1639.1412170972980.5905692337877691086;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 509 400;
					setLocation 8 22;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
				tell It;
					suppress;
					setTreeDrawer  #mesquite.trees.SquareLineTree.SquareLineTree;
					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
							branchLengthsToggle off;
							toggleScale on;
							toggleBroadScale off;
							toggleCenter on;
							toggleEven on;
							setFixedTaxonDistance 0;
						endTell;
						setEdgeWidth 4;
						showEdgeLines on;
						orientUp;
					endTell;
					setBackground White;
					setBranchColor Black;
					showNodeNumbers off;
					showBranchColors on;
					labelBranchLengths off;
					centerBrLenLabels on;
					showBrLensUnspecified on;
					showBrLenLabelsOnTerminals on;
					setBrLenLabelColor 0 0 255;
					setNumBrLenDecimals 6;
					desuppress;
					getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
					tell It;
						setColor Black;
						toggleColorPartition off;
						toggleColorAssigned on;
						toggleShadePartition off;
						toggleShowFootnotes on;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setDrawingSizeMode 0;
					toggleLegendFloat on;
					scale 0;
					toggleTextOnTree off;
					showWindow;
				endTell;
				desuppressEPCResponse;
				getEmployee #mesquite.trees.ColorBranches.ColorBranches;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
				tell It;
					setAlwaysOn off;
				endTell;
				getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
				tell It;
					colorByPartition off;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;
				tell It;
					setOn on;
					setDigits 4;
					writeAsPercentage off;
					toggleCentred off;
					toggleHorizontal on;
					toggleWhiteEdges on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings;
				tell It;
					setOn on;
					toggleCentred on;
					toggleHorizontal on;
					setFontSize 10;
					setOffset 0  0;
				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;