#NEXUS
[written Mon Aug 24 00:51:01 BRT 2015 by Mesquite  version 3.04 (build 725) at fernando-HP-Pavilion-15-Notebook-PC/127.0.1.1]

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=7;
	TAXLABELS
		'Escherichia coli YP_006125372.1 ' 'Moorella thermoacetica YP_431019.1' 'Geobacillus sp. Y4.1MC1 YP_003989194.1' 'Caldanaerobacter subterraneus yonseiensis_ERM92230.1' 'Thermoanaerobacter sp. YS13 THYS13_RS04655' 'Caldanaerobacter subterraneus pacificus_CDSM653_01582' 'Caldanaerobacter subterraneus tengcongensis_NP_623298.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=480;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Escherichia coli YP_006125372.1 '                       MENLALTTLLLPFIGALVVSFSPQRRAAEWGVLFAALTTLCMLSLISAFYQADKVAVTLTLVNVGDVALFGLVIDRVSTLILFVVVFLGLLVTIYSTGYLTDKNREHP-HNGTNRYYAFLLLFIGAMAGLVLSSTLLGQLLFFEITGGCSWALISYYQSDKAQRSALKALLITHIGSLGLYLAAATLFLQTGTFALSAMSELHGDARYLVYGGILFAAWGKSAQLPMQAWLPDAMEAPTPISAYLHAASKVKVGVYIFARAIIDGGNIPHVIGGVGMVMALVTILYGFLMYLPQQDMKRLLAWSTITQLGWMFFGLSLSIFGSRLALEGSIAYIVNHAFAKSLFFLVAGALSYSCGTRLLPRLRGVLHTLPLPGVGFCVAALAITGVPPFNGFFSKFPLFAAGFALSVEYWILLPAMILLMIESVASFAWFIRWFGRVVPGKPSEAVADAAPLPGSMRLVLIVLIVMSLISSVIAATWLQ
	'Moorella thermoacetica YP_431019.1'                     MVEYAVASILIPILGSVLAVIMPGSYVKRISPLFAFLTFASSLLLMIDFTRAGGASITQGLLQFGGMQVLGVTIDKVSVLIGFAVIFMGLLVCVYSLGYMTTSNKEHPVHGGTKRYYAFLLLFIGSMAGLVFSSTIIGLLVFFELTGVCSWGLIGFYDTPAARRAALKALIITHVASIGLYVAAIYLFINSGSFELAALAGLKDTAKVVVFLGILVASWGKSAQLPLHSWLPDAMVAPTPVSAYLHAASMVKVGAYIFARTLLSAGSVPQVIGYIGGIMAIVTLAYGFAMYFPQQDMKKLLAYSTIAQLSYIFLALSISVFGSSMAYKGAVAHIFNHAFAKGLFFLVAGALSYTTGTRMLPQLRGILSKMPLVGVSFAAAALAVGGTPPFNLFFSKFSIFVGGFEAAKNHPIVLLLVLVAVVESVGSFAWLLRWFGTCVMGKPSETVAGAITLPLSMKIVLLLLVVMTLISQYIALVFLG
	'Geobacillus sp. Y4.1MC1 YP_003989194.1'                 MVWYALGSILLPVLGSALILFIPERHVKKVSQFFSFLAFICGLLLLITFATTSN-SFTQDLLTISGINLFGVTIDTLSVLVNFMVVFIGWLICTYSAGYMNAGNREHPVKEGIPRFYAFMLLFIGSMSGLVFSSTLLGLLFFFEMTGLCSWNLIRFYGDQKSRRSALWAIILTHFASLGLYVAAAYVFISTGSFSVAALSKLTETGKIVAFIGILIASWGKSAQLPLHPWLPRAMVAPTPVSAYLHAASMVKVGVYIFARTVLEAGSVPQVIGEIGVIMAVVTMVYGFVMYFPQDDMKKLLAYSTIAQLSYIFLAVSLSIYGSKMAFDGAVAHIFNHAFAKGLFFLVAGALAYTTGTRRLSMLKGILKKTPVIGLGYIAAAMAITGVPPFNGFFSKFMIILAGFEIGIHHPLVLVLMIVTMIESVGSFIWILKWMGVNVLGAPSDAVANAAAPPLPIKFVLSVLIIMTLISQYIVFLLLS
	'Caldanaerobacter subterraneus yonseiensis_ERM92230.1'   MVWYALGSILLPLLGSLVVLFLPEQQVKRAGQLFSFLAFLCGLALLVSFALTGE-SFSRELVAINGVTCYGIIVDALSVLTNFLVVLIGWLICTYSAGYMSPDNREHPICEGINRFYSLMLLFIGSMAGVVFSSTLLGLLFFFEITGICSWSLIGFYGDEKSRKSALWAIALTHSAALGLYVATAYLYVKTGSFSVTALGKLTEAEKTIAFMGILIACWGKSAQIPFHPWLPRAMVAPTPVSAYLHAASMVKVGVYIYARTVLAAGKVPEVIGQVGAIMAVITMIYGFIMYFPQQDMKRLLAYSTITQLSYIFLAISIFILGSQMAFKGGVSHIFNHAFGKSLFFLVAGALSYTTGTRKLLMFRGILKKMPVVGLGYIAASIAITGVPPFNGFFSKIMIIISGFEIGRHNLLILILTIITVIESVGSFIWFLKWMGTNVFGTPSETVAIAGKPPLAIKFVLAFLIIMTLISQYIALALLS
	'Thermoanaerobacter sp. YS13 THYS13_RS04655'             MVWYALGSILLPLVGSLVVLFLSEQQVKKAGQLFSFLAFLCGLALLVSFALTGE-SFSRELVTINGVTCYGITVDALSVLTNFLVVLIGWLICTYSVGYMSPDNREHPICEGINRFYSLMLLFIGSMAGVVFSTTLLGLLFFFEITGICSWSLIGFYGDEKSRKSALWAIALTHSAALGLYVATAYLYVKTGSFSVTALGKLTEAEKTIAFIGILIACWGKSAQLPFHPWLPRAMVAPTPVSAYLHAASMVKVGVYIYARTVLAAGKVPAVIGQVGAIMAVITMIYGFIMYFPQQDMKRLLAYSTITQLSYIFLAISIFILGSQMAFKGGVAHIFNHAFGKSLFFLVAGALSYTTGTRKLLTFRGILKKMPVIGLGYIAASMAITGVPPFNGFFSKIMIIISGFEIGRHNLLILILTIITVIESVGSFIWFLKWMGTNVFGTPSETVATAGKPPLAIKFVLAFLIIMTLISQYIALALLS
	'Caldanaerobacter subterraneus pacificus_CDSM653_01582'  MVWYALGSILLPLVGSLVVLFLSEQQVKKAGQLFSFLAFLCGLALLVSFALTGE-SFSRELVAINGVTCYGITVDALSVLTNFLVVLIGWLICTYSAGYMSPDNREHPICEGINRFYSLMLLFIGSMAGVVFSTTLLGLLFFFEITGICSWSLIGFYGDEKSRKSALWAIALTHSAALGLYVATAYLYVKTGSFSVTALGKLTEAEKTIAFIGILIACWGKSAQLPFHPWLPRAMVAPTPVSAYLHAASMVKVGVYIYARTVLAAGKVPAVIGQVGAIMAVITMIYGFIMYFPQQDMKRLLAYSTITQLSYIFLAISIFILGSQMAFKGGVAHIFNHAFGKSLFFLVAGALSYTTGTRKLLMFRGILKKMPVIGLGYIAASMAITGVPPFNGFFSKIMIIISGFEISRHNLLILILTIITVIESVGSFIWFLKWMGTNVFGTPSETVATAGKPPLAIKFVLAFLIIMTLISQYIALALLS
	'Caldanaerobacter subterraneus tengcongensis_NP_623298.1' MVWYALGSILLPLVGSLVVLFLSEQQVKKAGQLFSFLAFLCGLALLVSFALTGE-SFSRELVAINGVTCYGITVDALSVLTNFLVVLIGWLICTYSAGYMSPDNREHPICEGINRFYSLMLLFIGSMAGVVFSTTLLGLLFFFEITGICSWSLIGFYGDEKSRKSALWAIALTHSAALGLYVATAYLYVKTGSFSVTALGKLTEAEKTIAFIGILIACWGKSAQLPFHPWLPRAMVAPTPVSAYLHAASMVKVGVYIYARTVLAAGKVPAVIGQVGAIMAVITMIYGFIMYFPQQDMKRLLAYSTITQLSYIFLAISIFILGSQMAFKGGVAHIFNHAFGKSLFFLVAGALSYTTGTRKLLMFRGILKKMPVIGLGYIAASMAITGVPPFNGFFSKIMIIISGFEISRHNLLILILTIITVIESVGSFIWFLKWMGTNVFGTPSETVATAGKPPLAIKFVLAFLIIMTLISQYIALALLS

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  480;

END;

BEGIN NOTES;

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

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  480;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  480;
END;

BEGIN TREES;
	Title 'Trees from "hyfD.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 'Escherichia coli YP_006125372.1 ',
[1] 		2 'Moorella thermoacetica YP_431019.1',
[2] 		3 'Geobacillus sp. Y4.1MC1 YP_003989194.1',
[3] 		4 'Caldanaerobacter subterraneus yonseiensis_ERM92230.1',
[4] 		5 'Thermoanaerobacter sp. YS13 THYS13_RS04655',
[5] 		6 'Caldanaerobacter subterraneus pacificus_CDSM653_01582',
[6] 		7 'Caldanaerobacter subterraneus tengcongensis_NP_623298.1';
	TREE tree_1 = (((((6:0.000001,7:0.000001)0.761000:0.002159,5:0.006375)0.853000:0.008729,4:0.017305)1.000000:0.23642,3:0.093721)1.000000:0.247762,2:0.250161,1:0.608557)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440388261554;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
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		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
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		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
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			tell It;
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				getWindow;
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					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
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					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 #7533584349174312660  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
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				endTell;
				setAssignedID 4831.1440388041597.5302052520133590777;
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					getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
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					tell It;
						setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
						tell It;
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							toggleCenter on;
							toggleEven on;
							setFixedTaxonDistance 0;
						endTell;
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						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;
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						toggleShadePartition off;
						toggleShowFootnotes on;
						toggleNodeLabels on;
						toggleCenterNodeNames off;
						toggleShowNames on;
						namesAngle ?;
					endTell;
				endTell;
					setTreeNumber 1;
					setTree '((2,((4,3),(6,(7,5)))),1);';
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					scale 0;
					toggleTextOnTree off;
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				getEmployee #mesquite.trees.ColorBranches.ColorBranches;
				tell It;
					setColor Red;
					removeColor off;
				endTell;
				getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
				tell It;
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				endTell;
				getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
				tell It;
					colorByPartition off;
				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles;
				tell It;
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					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;
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					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 #1770007937220156954 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
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					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
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					setLocation 51 24;
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					setFontSize 10;
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					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;
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				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;