#NEXUS
[written Mon Apr 16 09:45:59 CEST 2018 by Mesquite  version 3.40 (build 877) at PC-BORCHIELLINI/172.20.36.92]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=9;
	TAXLABELS
		'D.melanogaster_Bazooka/617-736  2621 bp' 'M.musculus_PAR3/585-684  2621 bp' 'A.digitifera/610-715 1299 aa 1299 bp' 'T.adhaerens_PAR3/415-521  2621 bp' 'M.leidyi_PAR3/504-607  2621 bp' 'O.lobularis_PAR3_G/424-516' 'P.ficiformis_PAR3/1024-1124' 'S.ciliatum_PAR3/866-975  2621 bp' 'O.minuta_PAR3/818-917  2621 bp' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=122;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'D.melanogaster_Bazooka/617-736  2621 bp' SREELTLHIPV--HDTEKAGLGVSVKGKTCSNLNASGSSASSGSNGLMKHDGDLGIFVKNVIHGGAASRDGRLRMNDQLLSVNGVSLRGQNNAEAMETLRRAMVNTPGKHPGTITLLVGRKI
	'M.musculus_PAR3/585-684  2621 bp'       --EFLTFEVPL--NDSGSAGLGVSVKGNR-SKENHA----------------DLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESLLGKANQEAMETLRRSMSTEGNKR-GMIQLIVARRI
	'A.digitifera/610-715 1299 aa 1299 bp'   --QVLTFKIPL--DLSGAAGLGVSVKGKSHGTPDQGRDSPQ-----------DKGIFCKSIIPGGAAAKDGRLRPDDQLLRVNGKSLVGLTNQTAMGTLRVAMQSTRPGQ-AFIDVTIARAQ
	'T.adhaerens_PAR3/415-521  2621 bp'      M-HTEIIQVKL--RTSPAGGLGINVKGRILNEDSSSPTGRK-----------DAGIFIKAIMPGSAADQDGRLLKDDRVIAVNNISLNHLANDEAMSTLKAIMKDAIERA-GFVTFAVLRHT
	'M.leidyi_PAR3/504-607  2621 bp'         --TRLSLDVSLVAPDGRPVGLGISVKGKSMSIRGEPRR--------------DYGIFIKSILKGGAADLDGRLKADDQLLSADGQTLKGLTNKEAMQSLKQALERAGKM--PSLSLVVSRKD
	'O.lobularis_PAR3_G/424-516'             --QTLHFNIPL--NLSGSNSLGISVKGKT-STHSAAHAAAK----------------------DDSVSDDGRLMPNDQILSINGENLEGKSNASAMECLRTAMQSAAMK--DHIDLIVKRKI
	'P.ficiformis_PAR3/1024-1124'            --TVMSLNIHL--NNCGLAGLGVTVHCRS-SKKKGG----------------DVGVYIKSISPGGGAAQEGTLRVNDRILSVNGLSLAHMNNADALEALKRGLSQAKPGEDAKIQLTIARTT
	'S.ciliatum_PAR3/866-975  2621 bp'       VRKQLLFTIPL--TSSGSAGLGISVKGKT-AMSSEQRTAGEQG-------DVGHGIYIKNVLPGGAAAKDGRLQPSDRLVSINGENLSSLSDYEAFESLRKCMAGASQR--PSIDLVIERRS
	'O.minuta_PAR3/818-917  2621 bp'         --KIQPLLIPL-----TETGLGVSVRGKTRMNTNSKPQ--------------EGGIFVKVIVQGGAADKDGRLKPNDQILSINGCVLVGQSNQEAMKTLKYGLEKISPEQ-PVIKLVVLKKP

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  122;

END;

BEGIN NOTES;

	TAXABITS   NAME = newlyAddedTaxon on =  1 -  9;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  122;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  122;
END;

BEGIN TREES[!'Parameters: Tree search criterion: minimize Tree value using character matrix'];
	Title 'Trees from Mesquite''s heuristic search';
	ID 0162cd6aa6da16;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 'D.melanogaster_Bazooka/617-736  2621 bp',
[1] 		2 'M.musculus_PAR3/585-684  2621 bp',
[2] 		3 'A.digitifera/610-715 1299 aa 1299 bp',
[3] 		4 'T.adhaerens_PAR3/415-521  2621 bp',
[4] 		5 'M.leidyi_PAR3/504-607  2621 bp',
[5] 		6 'O.lobularis_PAR3_G/424-516',
[6] 		7 'P.ficiformis_PAR3/1024-1124',
[7] 		8 'S.ciliatum_PAR3/866-975  2621 bp',
[8] 		9 'O.minuta_PAR3/818-917  2621 bp';
	TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = ((((((4,2),(3,7)),5),9),(8,6)),1)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = (((8,6),1),((((4,2),(3,7)),5),9))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = ((8,6),(((((4,2),(3,7)),5),9),1))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = (((((4,2),(3,7)),5),((8,6),1)),9)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = ((((4,2),(3,7)),5),(((8,6),1),9))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = ((6,(((((4,2),(3,7)),5),9),1)),8)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = (6,(8,(((((4,2),(3,7)),5),9),1)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = ((5,(((8,6),1),9)),((4,2),(3,7)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = (5,(((4,2),(3,7)),(((8,6),1),9)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = (((4,2),(5,(((8,6),1),9))),(3,7))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = ((4,2),((5,(((8,6),1),9)),(3,7)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = ((3,((4,2),(5,(((8,6),1),9)))),7)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = (3,(((4,2),(5,(((8,6),1),9))),7))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = ((2,((5,(((8,6),1),9)),(3,7))),4)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = (2,(4,((5,(((8,6),1),9)),(3,7))))[% ] [% ] [%  setBetweenBits = selected ];

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1523864759774;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 1197493745121785428;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 6227846164039778272;
			mqVersion 340;
			checksumv 0 3 1208439379 null  getNumChars 122 numChars 122 getNumTaxa 9 numTaxa 9   short false   bits 786431   states 786431   sumSquaresStatesOnly 2.72655813113E12 sumSquares 2.72655813113E12 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 201;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 464;
			setLocation 8 8;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #1197493745121785428  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					setTreeBlockID 0162cd6aa6da16;
					toggleUseWeights off;
				endTell;
				setAssignedID 2062.1523864745254.8329169140266246791;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 499 392;
					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;
					toggleShow consensusFrequency;
					toggleShow bootstrapFrequency;
					toggleShow posteriorProbability;
					toggleShow consensusFrequency;
					toggleShow posteriorProbability;
					toggleShow bootstrapFrequency;
					setDigits 4;
					setThreshold ?;
					writeAsPercentage off;
					toggleCentred off;
					toggleHorizontal on;
					toggleWhiteEdges on;
					toggleShowOnTerminals 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;
					toggleShowOnTerminals on;
				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #6227846164039778272 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 499 392;
					setLocation 8 8;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
					endTell;
					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
					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.AlterData.AlterData;
				tell It;
					toggleBySubmenus off;
				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 16 6 1 1;
					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;