#NEXUS
[written Thu Dec 24 10:44:53 CST 2015 by Mesquite  version 3.04 (build 725) at PRD-AA01495/192.168.228.13]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=10;
	TAXLABELS
		Chlamydomonas_reinhardtii Glycine_max Medicago_truncatula Micromonas_pusilla_CCMP1545 Oryza_sativa Phaeocystis_antarctica Phaeocystis_globosa Physcomitrella_patens Theobroma_cacao Zea_mays 
	;

END;


BEGIN CHARACTERS;
	TITLE  'Matrix in file "D.nexus"';
	DIMENSIONS  NCHAR=233;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Chlamydomonas_reinhardtii    MAVMMRTQAPAATR---------------ASSRVAVAARPAA----RRAVVVRAEAEAAP----AAAKKAAEKPA-WTVPTLNPDTPSPIFGGSTGGLLRKAQTEEFYVITWEAKKEQIFEMPTGGAAIMRQGPNLLKFGKKEQCLALTTQLRNKFKLT-PCFYRVFPDGKVQYLHPADGVYPEKVNAGRVGANQNMRRIGQNVNPIKVKFSGR------------MMSPAEI
	Glycine_max                  MAMATQASLFTPPLSGLKPSDRATAPWKQSSTLSFSTSKPLKF---SRTIRAAATDQTTE------------APVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWDSPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIGKNVSPIEVKFTGK--------------QPYDL
	Medicago_truncatula          MAMATQASLFTPPLSSPK-------PWKQPSTLSFISLKPIKFT--TKTTKISAADEKTEAASVTTKEEAPAAPVGFTPPELDPNTPSPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMREGPNLLKLARKEQCLALGNRLRSKYKIK-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGQNFRSIGKNVSPIEVKFTGK--------------QPFDV
	Micromonas_pusilla_CCMP1545  MAAISQAQCVV-NVTAAAPAARSRVALRASFSGKSVAAKPAYFAAKRQSVLVRAEEKTAE----KAVEKKEEAP--WSPPKLNPNTPSPIFGGSTGGLLRKAQVEEFYVLTWEAPKEMIFEMPTGGAAIMRKGPNLLKLARKEQCLALLNSMRAKNKIN-GCVYRVFPSGEVQYLHPKDGVYPEKVNKGRVGANNNMRSIGKNANPASIKFGGKLGSDGLASDGAGFSRVFDQ
	Oryza_sativa                 MAMATQASAAKCHL---------LAAWAPAKPRSSTLSMPTSRA--PTSLRAAAEDQPAA----AATEEKKPAPAGFVPPQLDPNTPSPIFGGSTGGLLRKAQVEEFYVITWTSPKEQVFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIN-YQFYRVFPNGEVQYLHPKDGVYPEKVNAGRQGVGQNFRSIGKNVSPIEVKFTGK--------------NVFDI
	Phaeocystis_antarctica       -----------------------------------------------------------------------------MTDILDLQIASPTFGGSTGGWLRAAETEEKYAITWTSKKEQIFEMPTSGSAIMQKGENLLYLAKKEQCLALGTQLRTSFKINDYKIYRIFPNSEVQYLHPKDGVFPEKLNAGRLGVGNVMHSIGKNAQPVNVKFTGK--------------NTFD-
	Phaeocystis_globosa          -----------------------------------------------------------------------------MTDILDLQIASPTFGGSTGGWLRAAETEEKYAITWTSKKEQIFEMPTSGSAIMQKGENLLYLAKKEQCLALGTQLRTSFKVNDYKIYRIFPNSEVQYLHPKDGVFPEKLNAGRLGVGNVMHSIGKNAQPVNVKFTGK--------------NTFD-
	Physcomitrella_patens        ---MAQAGAAPDGV----------------------------------------ADQKPD---------AKEAPKGFTPPTLNADTPAPIFGGSTGGLLRKAQVEEFYVITWESPKEQIFEMPTGGAAIMRSGPNLLKLARKEQCLALGARLRTKFKIQ-YQFYRVFPNGEVQYLHPKDGVYPEKVNAGRSPVGVNNRSIGKNANPAELKFAQK--------------QAYDL
	Theobroma_cacao              --MATQAGLFTPTISTPK----SLVPWKPSWSFSFATPKSLNLSMAHSTIRAAAADQEAA--------TKEEAPVGFTPPELDPNTPSPMFSGSTGGLLRKAQVEEFYVITWDSPREQIFEMPTGGAAIMRQGPNLLKLARKEQCLALGTRLRSKYKIN-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGRQGVGQNFRSIGKNVSPIEVKFTGK--------------QVYDL
	Zea_mays                     MAMATQASAATRHL--------LAAAWAP-------AAKPRQL---SSQLALPSSSSRGPAPLRASTEEAVEAPKGFVAPQLDPSTPSPIFGGSTGGLLRKAQVEEFYVITWTSPKEQVFEMPTGGAAIMREGPNLLKLARKEQCLALGTRLRSKYKIT-YQFYRVFPNGEVQYLHPKDGVYPEKVNPGREGVGQNFRSIGKNVNPIDVKFTGK--------------ATFD-

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED  (CHARACTERS = 'Matrix in file "D.nexus"')  =  unord:  1 -  233;

END;

BEGIN CODONS;
	CODESET * UNTITLED  (CHARACTERS = 'Matrix in file "D.nexus"')  =  universal:  1 -  233;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED  (CHARACTERS = 'Matrix in file "D.nexus"')  =  'Mk1 (est.)':  1 -  233;
END;

BEGIN TREES;
	Title Imported_trees;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 Chlamydomonas_reinhardtii,
[1] 		2 Glycine_max,
[2] 		3 Medicago_truncatula,
[3] 		4 Micromonas_pusilla_CCMP1545,
[4] 		5 Oryza_sativa,
[5] 		6 Phaeocystis_antarctica,
[6] 		7 Phaeocystis_globosa,
[7] 		8 Physcomitrella_patens,
[8] 		9 Theobroma_cacao,
[9] 		10 Zea_mays;
	TREE Imported_tree_1 = (((((2:0.03699051,3:0.07633818)0.9130:0.03083015,9:0.11046536)0.9780:0.04173878,(5:0.09476209,10:0.11050104)0.8440:0.02986203)0.5310:0.01570603,8:0.12564356)0.7230:0.05053558,(6:0.0,7:0.00837689)1.0000:0.21680928,(1:0.25188863,4:0.21194849)0.9420:0.06762922);

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1450925093122;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 6989048315910566846;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 2648831916297079194;
			mqVersion 304;
			checksumv 0 3 1352365586 null  getNumChars 233 numChars 233 getNumTaxa 10 numTaxa 10   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 1.9625395938201E13 sumSquares 1.9625395938201E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 209;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 472;
			setLocation 8 8;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #6989048315910566846  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1395.1450924049382.2553490242990869846;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 491 400;
					setLocation 8 8;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setActive;
					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;
					togglePrintName on;
					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;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #2648831916297079194 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					getTable;
					tell It;
						rowNamesWidth 210;
					endTell;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 491 400;
					setLocation 8 8;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
					colorCells  #mesquite.charMatrices.ColorByState.ColorByState;
				tell It;
					setStateLimit 9;
					toggleUniformMaximum on;
				endTell;
					colorRowNames  #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
					colorColumnNames  #mesquite.charMatrices.CharGroupColor.CharGroupColor;
					colorText  #mesquite.charMatrices.NoColor.NoColor;
					setBackground White;
					toggleShowNames on;
					toggleShowTaxonNames on;
					toggleTight off;
					toggleThinRows off;
					toggleShowChanges off;
					toggleSeparateLines off;
					toggleShowStates on;
					toggleAutoWCharNames off;
					toggleAutoTaxonNames off;
					toggleShowDefaultCharNames off;
					toggleConstrainCW on;
					toggleBirdsEye off;
					toggleShowPaleGrid off;
					toggleShowPaleCellColors off;
					toggleShowPaleExcluded off;
					togglePaleInapplicable on;
					toggleShowBoldCellText off;
					toggleAllowAutosize off;
					toggleColorsPanel off;
					toggleLinkedScrolling on;
					toggleScrollLinkedTables off;
				endTell;
				showWindow;
				getWindow;
				tell It;
					forceAutosize;
				endTell;
				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
				tell It;
					togglePanel off;
				endTell;
				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
				tell It;
					autotabOff;
				endTell;
				getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
				tell It;
					gapCosts 8 3 2 2;
					subCosts  5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5;
				endTell;
				getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		endTell;
end;