#NEXUS
[written Mon Aug 24 14:09:53 BRT 2015 by Mesquite  version 3.04 (build 725) at fernando-To-be-filled-by-O-E-M/127.0.1.1]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=11;
	TAXLABELS
		'Caldanaerobacter subterraneus pacificus_CDSM653_01579' 'Caldanaerobacter subterraneus tengcongensis_NP_623295.1' 'Caldanaerobacter subterraneus yonseiensis_ERM92228.1' 'Escherichia coli NP_416984.1' 'Escherichia coli YP_006125564.1' 'Geobacillus sp. Y4.1MC1 YP_003989197.1' 'Geobacillus thermoglucosidasius YP_004587928.1' 'Moorella thermoacetica YP_431016.1' 'Thermacetogenium phaeum YP_006921302.1' 'Thermoanaerobacter sp. YS13 THYS13_RS04625' 'Thermococcus onnurineus TON_1024' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=285;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Caldanaerobacter subterraneus pacificus_CDSM653_01579'  ----MEP------------EAKLQELKAKLKNVIKRSAYLYRVDCGGCNGCEIEIFAAISPVYDPERFGIKIVSSPRHADILLFTGPMTRAMRLPAIRAYKAAPDPKIVVAYGACGCSGGIFHDCYCVWGGIDKFF-----------PVDVYIPGCPPTPAATLYGLAVALDLLHQKIKGEQFVETEVT-----PVPAKYEGVCPDLAKDIEREARRLSGYLHGRRIAAQYLEFVKQGDPLSVDRKIKELVKQQKDPRLAEIFLSLHKIYM------ERVGHDAG
	'Caldanaerobacter subterraneus tengcongensis_NP_623295.1' ----MEP------------EAKLQELKAKLKNVIKRSAYLYRVDCGGCNGCEIEIFAAISPVYDPERFGIKIVSSPRHADILLFTGPMTRAMRLPAIRAYKAAPDPKIVVAYGACGCSGGIFHDCYCVWGGIDKFF-----------PVDVYIPGCPPTPAATLYGLAVALDLLHQKIKGEQFVETEVT-----PVPAKYEGVCPDLAKDIEREARRLSGYLHGRRIAAQYLEFVKQGDPLSVDRKIKELVKQQKDPRLAEIFLSLHKIYM------ERVGHDAG
	'Caldanaerobacter subterraneus yonseiensis_ERM92228.1'   ----MEP------------EAKLQELKAKLRNVIKRSAYLYRVDCGGCNGCEIEIFAAISPVYDPERFGIKIVSSPRHADILLFTGPMTRAMRLPAIRAYKAAPDPKIVVAYGACGCSGGIFHDCCCVWGGIDKFF-----------PVDVYIPGCPPTPAATLYGLALALDLLHQKIKGEQFVETEVT-----PVPTKYEGVCPDIAKDIEREARRLSGYLHGRRIAAQYLEFVRQGDPLSVDRKIKELVKQQKDPRLAEIFLSLHKIYM------ERVGHDAG
	'Escherichia coli NP_416984.1'                           ----MSPVLTQHVSQPITLDEQTQKMKRHLLQDIRRSAYVYRVDCGGCNACEIEIFAAITPVFDAERFGIKVVSSPRHADILLFTGAVTRAMRMPALRAYESAPDHKICVSYGACGVGGGIFHDLYSVWGGSDTIV-----------PIDVWIPGCPPTPAATIHGFAVALGLLQQKIHAVDYRDPTGV-----TMQPLWPQIPPSQRIAIEREARRLAGYRQGREICDRLLRHLSD-DP--TGNRVNTWLRDADDPRLNSIVQQLFRV--------LRGLHD--
	'Escherichia coli YP_006125564.1'                        MSNLLGPRDANGIPVPMTVDESIASMKASLLKKIKRSAYVYRVDCGGCNGCEIEIFATLSPLFDAERFGIKVVPSPRHADILLFTGAVTRAMRSPALRAWQSAPDPKICISYGACGNSGGIFHDLYCVWGGTDKIV-----------PVDVYIPGCPPTPAATLYGFAMALGLLEQKIHARGPGEQDEQ-----PAEILHGEMVQPLRVKVDREARRLAGYRYGRQIADDYLTQLGQGE-----EQVARWLEAENDPRLNEIVSHLNHVVEE-----ARIR----
	'Geobacillus sp. Y4.1MC1 YP_003989197.1'                 ----MDQ------------EVKLADLKAKLKNVIKRSVYVYRVDCGGCNGCEIEIFSAISPTFDAERFGIKVVPTPRHADILLITGPMTRAMRLPAIRAYQAAPDPKIVVAYGACSCSGGIFHDCYGVWGGAESAF-----------PVDVYIPGCPPTPAATLYGLAIALDLLQQKIKGEQFVEEDVT-----HVTPKYDGVSPDLAKELEWEARRLSGYLQGRRIAAQYIEFIKEGNPLVVDQKIKELVKQEKDPRLAEVILKLHKIYM------ERVSHHAG
	'Geobacillus thermoglucosidasius YP_004587928.1'         ----MDQ------------EVKLADLKAKLKNVIKRSVYVYRVDCGGCNGCEIEIFSAISPTFDAERFGIKVVPTPRHADILLITGPMTRAMRLPAIRAYQAAPDPKIVVAYGACSCSGGIFHDCYGVWGGAESAF-----------PVDVYIPGCPPTPAATLYGLAMALDLLQQKIKGEQFVEEDVT-----HVTPKYDGVSPDLAKELEWEARRLSGYLQGRRIAAQYIEFIKEGNPLVVDQKIKELVKQEKDPRLAEVILKLHKIYM------ERVSHHAG
	'Moorella thermoacetica YP_431016.1'                     ----MEQ------------EVKLAELKAKLKNVIKRSVYVYRVDCGGCNGCEIEIFATISPVYDPERLGFKVVASPRHADILLFTGPMTRAMRLPAIRAYQAAPDPKIVVAYGTCGCSGGIFHDCYSVWGGTGSIF-----------PVDVYIPGCPPTPGATIYGLGLALDLLQQKMKGEQYTEKEVA-----RITSQYAGVSPDLARDIEREARRLSGYLHGRRITEKYLQFVRE-DPLAVDQKIKELVKQEKDSRLAEVYLSLHKIYLDYLGKTEKAGHHAG
	'Thermacetogenium phaeum YP_006921302.1'                 ----MNTAEQTGAAQ----QEQIEALKAKLLHDIRRSVYVYRIDCGGCNGCEIEIFASLTPLFDVERFGIKVVPSPRHADVLVYTGPMTRAMRLPALRAYRAAPDPKIVVAYGACGCSGGIFHDSYAVWGGAENLF-----------PVDLYIPGCPPSPYATIYGFATVLGLLEQKIRGQQHRESEEEKGVELTVPA---GINPNLRKEIERTARRLCGYWQGKRIAADYFKLLAESPDDVLDYRLEGYLSRKGDPRLTEVYRAIHRIYR------EWVNSRA-
	'Thermoanaerobacter sp. YS13 THYS13_RS04625'             ----MEP------------EAKLQELKAKLKNVIKRSAYLYRVDCGGCNGCEIEIFAAISPVYDPERFGIKIVSSPRHADILLFTGPMTRAMRLPAIRAYKAAPDPKIVVAYGACGCSGGIFHDCYCVWGGIDKFF-----------PVDVYIPGCPPPPAATLYGLALALDLLHQKIKGEQFVETEVT-----PVPAKYEGVCPDQAKDIEREARRLSGYLHGRRIAAQYLEFVKQGDPLSVDRKIKELVKQQKDPRLAEIFLSLHKIYM------ERVGHDAG
	'Thermococcus onnurineus TON_1024'                       --------------------------------MVKNSLWVFHLNSGSCNGCDIEILNIFAPRNDVERLGIKLVGSPRHADAIAFTGPITRECLPKVIDALKAVPEPKVVLAIGACACGGGIWYDTYSVIGGVKELYRILKEEYNMEPPATVFIPGCPPKPEAIIYGVAVASGMLESKQKKTVYVEPEES-------VANEKLMIAELISETEKTRHFMPGIV-------------------------------------------------------IRGVEDEP

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  285;

END;

BEGIN NOTES;

	TAXABITS   TAXA = Taxa NAME = newlyAddedTaxon on =  1 -  11;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  285;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  285;
END;

BEGIN TREES;
	Title 'Trees from "hyfI.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		n0 'Caldanaerobacter subterraneus pacificus_CDSM653_01579',
[1] 		n1 'Caldanaerobacter subterraneus tengcongensis_NP_623295.1',
[2] 		n2 'Caldanaerobacter subterraneus yonseiensis_ERM92228.1',
[3] 		n3 'Escherichia coli NP_416984.1',
[4] 		n4 'Escherichia coli YP_006125564.1',
[5] 		n5 'Geobacillus sp. Y4.1MC1 YP_003989197.1',
[6] 		n6 'Geobacillus thermoglucosidasius YP_004587928.1',
[7] 		n7 'Moorella thermoacetica YP_431016.1',
[8] 		n8 'Thermacetogenium phaeum YP_006921302.1',
[9] 		n9 'Thermoanaerobacter sp. YS13 THYS13_RS04625',
[10] 		n10 'Thermococcus onnurineus TON_1024';
	TREE tree_1 = (((((((n1:0.000001,n0:0.000001)0.787000:0.00644,(n9:0.012964,n2:0.019421)0.000000:0.000001)0.983000:0.091431,n7:0.126427)0.761000:0.038147,(n6:0.000001,n5:0.006107)0.984000:0.097409)0.709000:0.045544,n10:1.360241)0.512000:0.082992,n8:0.222907)0.990000:0.192858,n3:0.244361,n4:0.206019)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440436193267;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 7151813393984084523;
			tell It;
				setSelected  11;
				setDefaultOrder  1 0 3 9 10 6 5 4 8 2 7;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 3810971818940258636;
			mqVersion 304;
			checksumv 0 3 2662522448 null  getNumChars 285 numChars 285 getNumTaxa 11 numTaxa 11   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 3.8741265747198E13 sumSquares 3.8741265747198E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
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			setResourcesState false false 287;
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			setFontIncExp 0;
			setSize 1518 464;
			setLocation 109 253;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #7151813393984084523 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #7151813393984084523;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1231 392;
					setLocation 109 253;
					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;
		endTell;
		getEmployee  #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
		tell It;
			makeTreeWindow #7151813393984084523  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 1843.1440436161535.7298149206467889425;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1231 392;
					setLocation 109 253;
					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;
					setTree '((((((2:0.000001,1:0.000001)0.787000:0.00644,(10:0.012964,3:0.019421)0.000000:0.000001)0.983000:0.091431,8:0.126427)0.761000:0.038147,(7:0.000001,6:0.006107)0.984000:0.097409)0.709000:0.045544,(9:0.222907,(4:0.244361,5:0.206019)root:0.192858)0.990000:0.082992)0.512000:0.6801205,11:0.6801205);';
					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 #3810971818940258636 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1231 392;
					setLocation 109 253;
					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.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;