#NEXUS
[written Mon Apr 16 09:44:11 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/308-398' 'M.musculus_PAR3/269-363' 'A.digitifera/340-433' 'T.adhaerens_PAR3/221-237' 'M.leidyi_PAR3/272-361' 'O.lobularis_PAR3_G/182-275' 'P.ficiformis_PAR3/760-854' 'S.ciliatum_PAR3/489-583' 'O.minuta_PAR3/424-512' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=99;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'D.melanogaster_Bazooka/308-398' KDGEMLLIINEYGSP--LGLTALPDKEHGG---GLLVQHVEPGSRAE--RGQLRRDDRILEINGIKLIGLTESQVQEQLRRALES-SELRVRVLRGDRN
	'M.musculus_PAR3/269-363'       DDMVKLVQVPNDGGP--LGIHVVPFSARGGRTLGLLVKRLEKGGKAE-QENLFHENDCIVRINDGDLRNRRFEQAQHMFRQAMRA-RVIWFHVVPAANK
	'A.digitifera/340-433'          EPDMLTIELKRDNSIEGLGFTVAGYRTADGRELGLIVRDISPSGCAA-RDGRLEIADRIVEVNGWSLMDIPNERAEEIFAAAIKS-PTVSLGISRS---
	'T.adhaerens_PAR3/221-237'      --------------------------TSDDENKGKILDKIGKT--------------------------------------------------------
	'M.leidyi_PAR3/272-361'         APETLKIEIVRDNLP--LGCVV---RHMDGRLPGLYIMSVDAGSAAE-RDGTLKLGDKILEVNGVDLSVMPSVSVVDVYNEMTST-AQVRLTVQRLP--
	'O.lobularis_PAR3_G/182-275'    GDDVRVVDIKKLGDM--LGIRAHGYKSSGGKDMGIFVQEIDKAKCKTLGDEPLLVTDRIVKINGKPVGDLSNKEALEVLAETSRNFIQIQLGVVRT---
	'P.ficiformis_PAR3/760-854'     EHKLHIVELLRGTEP--LGITLVSY-TSQGKDLGVFISEMDSEGFAA-TSGKLQVSDRILACNGEDFCKESNKRVEERFLDMATNEPLLRMAISRGLLL
	'S.ciliatum_PAR3/489-583'       GQEVADIELSCRSSKDEAGVFVRGYRTSDDRDIGVFVHDILPGSVAA-ENGLIRIADRLICVNGIDLTELSNNQAVALFQDAVRK-GNMKLQVSRAL--
	'O.minuta_PAR3/424-512'         IPKDHNLSLPRTDSP--LSISLATNKNNSN---APVDTRNEYTNTLD-NNTLVQEDPSNVEVRTLPLVTPPIQQPEHHIDKVIES--AIELPEERPI--

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  99;

END;

BEGIN NOTES;

	TAXABITS   NAME = newlyAddedTaxon on =  1 -  9;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  99;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  99;
END;

BEGIN TREES[!'Parameters: Tree search criterion: minimize Tree value using character matrix'];
	Title 'Trees from Mesquite''s heuristic search';
	ID 0162cd69011810;
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 'D.melanogaster_Bazooka/308-398',
[1] 		2 'M.musculus_PAR3/269-363',
[2] 		3 'A.digitifera/340-433',
[3] 		4 'T.adhaerens_PAR3/221-237',
[4] 		5 'M.leidyi_PAR3/272-361',
[5] 		6 'O.lobularis_PAR3_G/182-275',
[6] 		7 'P.ficiformis_PAR3/760-854',
[7] 		8 'S.ciliatum_PAR3/489-583',
[8] 		9 'O.minuta_PAR3/424-512';
	TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = (8,(5,((((1,2),(7,6)),(9,4)),3)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = ((5,8),((((1,2),(7,6)),(9,4)),3))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = (5,(8,((((1,2),(7,6)),(9,4)),3)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = (((((1,2),(7,6)),(9,4)),(5,8)),3)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = ((((1,2),(7,6)),(9,4)),((5,8),3))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = (((9,4),((5,8),3)),((1,2),(7,6)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = ((9,4),(((1,2),(7,6)),((5,8),3)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = (((1,2),((9,4),((5,8),3))),(7,6))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = ((1,2),(((9,4),((5,8),3)),(7,6)))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = ((4,(((1,2),(7,6)),((5,8),3))),9)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = (4,(9,(((1,2),(7,6)),((5,8),3))))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = ((7,((1,2),((9,4),((5,8),3)))),6)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = (7,(((1,2),((9,4),((5,8),3))),6))[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = ((2,(((9,4),((5,8),3)),(7,6))),1)[% ] [% ] [%  setBetweenBits = selected ];
	TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = (2,(1,(((9,4),((5,8),3)),(7,6))))[% ] [% ] [%  setBetweenBits = selected ];

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1523864651804;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 1339927270710037916;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 158407292966068188;
			mqVersion 340;
			checksumv 0 3 822502702 null  getNumChars 99 numChars 99 getNumTaxa 9 numTaxa 9   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 3.646356276829E12 sumSquares 3.646356276829E12 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
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			suppress;
			setResourcesState false false 201;
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			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #1339927270710037916  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					setTreeBlockID 0162cd69011810;
					toggleUseWeights off;
				endTell;
				setAssignedID 1680.1523864635944.6254802972108916987;
				getTreeWindow;
				tell It;
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					setAnnotationSize 20;
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					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;
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				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 #158407292966068188 #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;
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				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;