#NEXUS
[written Mon Aug 24 00:40:20 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=11;
	TAXLABELS
		'Thermococcus onnurineus TON_1022' 'Thermacetogenium phaeum YP_006921296.1' 'Geobacillus thermoglucosidasius YP_004587923.1' Geobacillus_sp._Y4.1MC1_YP_003989191.1 'Moorella thermoacetica YP_431022.1' 'Thermoanaerobacter sp. YS13 THYS13_RS04685' 'Caldanaerobacter subterraneus pacificus_CDSM653_01585' 'Caldanaerobacter subterraneus tengcongensis_NP_623301.1' 'Caldanaerobacter subterraneus yonseiensis_ERM92233.1' 'Escherichia coli YP_006125567.1' 'Escherichia coli YP_006125371.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=318;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Thermococcus onnurineus TON_1022'                       --------MNAVYAALNLIFIVLFAPLLDGIERKVKARLQSRQGPPLIQTWLDLLKLFRRPNVRPRESVRWLFEPAPAIALVSVLAASLFIPSL-LPGSLDTWGDIIAFIYLSTLSAVAIALGAFSTGSPYAQIGSHREVSIIMAEEFSLAFIVAALAASSG----GLSFSRLFPLQLK---VSTITGALAFAVMAYVAGARIPFDVAEAEPEIVEGPFIEFSGKGLGMLKLSIYVKRLLLTTILLNFFLPQDGT---------VRVLVYVIGLVIISVVYASIEAHYGRFRTKDAARFLKRFAIVGILSWILGVVGW
	'Thermacetogenium phaeum YP_006921296.1'                 ----MFDVNLFLLGILQAVFVVLAAPLLAGFARVLRAKMHSRTGPPILQYYYDLWKLLKRQDVSPAPAT-WVYRLTPYIVFSCAFLMAMIVPMVTLEAPLGYAGDLIVVIYLLAAIRFFTALSGIDSGSGFAGVGSIRELALSVLVEPALILVLLIMALFAGSTNLGSISLMIAQGEIPYTSPAVWLGMAALAVVSFVEMGKLPFDLAEAEQELQEGPLTEYSGRRLAVLEWGLFMKQVAVASLFLAVFFPFGSAASLSPPAVMAGLAFFLIKLAVCYFLAAVVENSMCRLTIYKAPGATWVALGIALLSFVFYLVEI
	'Geobacillus thermoglucosidasius YP_004587923.1'         ----MPEMKLLLIGLVQAVFLLLVAPFFTGLSRVLRAKVHSRKGPSILQDYRDIFKLIKRQEVVPAQSS-WVFRITPYVIMATMLLIAMIIPVLTLQAPLGMVGDLIVIVYLFTVFRFFFSIAGLDSGSSFAGIGASREMALGVLVEPTIILVLFVVALLSGSTDLGIISQKMATGEISYLSPAVLLGMVAFAVATFIESGKIPFDLAEAEAEIQEGPLTEYSGRSLAILKWSLGLKQMVVNALYLAIFFPFGNAAVVTPSAILVSMVLFLLKVVVIYVVAALLENSMARFVLFKTPAVTWVVFGIAMLSYVFYMVNI
	Geobacillus_sp._Y4.1MC1_YP_003989191.1                   ----MPEMKLLLIGLVQAVFLLLVAPFFTGLSRVLRAKAHSRKGPSILQDYRDIFKLIKRQEVVPAQSS-WVFRITPYVIMATMLLIAMIIPVLTLQAPLGMVGDLIVIVYLFTVFRFFFSIAGLDSGSSFAGIGASREMALGVLVEPTIILVLFVVALLSGSTDLGIISQKMATGEISYLSPAVLLGMVAFAVATFIESGKIPFDLAEAEAEIQEGPLTEYSGRSLAILKWSLGLKQMVVNALYLAIFFPFGNAAVVTPSAILVSMVLFLLKVVVIYVVAALLENSMARFVLFKTPAVTWVVFGIAMLSYVFYMVNI
	'Moorella thermoacetica YP_431022.1'                     ----MPGIKLFLVGLMQALLVLLVAPLFAGLTRVLRARLHSRKGASIFQDYRDIFKLIKRQEVVPAQAS-WVFRFTPYVVMATTLLIAMVIPILTLQSPLGMAGDLIAVVYLFALLRFFFAVAGLDSGSGFAGIGASREMVLAILVEPTIILVLFVLALLTGSTDLGAISQKVAFGSISYYRPAVWLGMLAFAVATFIETGKLPFDLAEAEQELQEGPLTEYSGRSLAILKWSLSMKQVVVIALFLAVFFPFGSAAAVSTSSLLVSAAAFLLKVTGFYVIAALMENSSARLIIYKAPEVTWLAFGIALLSFVFYLVNV
	'Thermoanaerobacter sp. YS13 THYS13_RS04685'             ----MLDDKLFFVGLLQALLVMAVTPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDVGVITQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNVAVVNGFSILMSTAVFLLKVAIFYVIVALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
	'Caldanaerobacter subterraneus pacificus_CDSM653_01585'  ----MLDGKLFFVGLLQALLLMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
	'Caldanaerobacter subterraneus tengcongensis_NP_623301.1' ----MLDGKLFFVGLLQALLLMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLFALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFRAHEVTWAAFGIALLSFVFFLVNV
	'Caldanaerobacter subterraneus yonseiensis_ERM92233.1'   ----MLDGKLFFVGLLQALLVMAVAPFFSGFARVLRAKIHSRKGPSIFQDYRDIFKLIKRQRVVPAQSS-WIFCLTPYVMMATILLIAMMTPILTLQSPLRMVGDLIAIVYLYALGRFFFAAAGLDSGSGFAGIGASREMTLAALVEPTIILVLFVMGLLAGSTDIGVISQKVATGEISYYSPTVWLAMAAFSIAAFIETGKLPFDLAEAEQEIQEGPLTEYSGGSLALLKWSLSMKQVVVIALFMAIFFPFGNAAVVNGFSILMSTAVFLLKVAIFYVIAALLENSMARLLLFMAPEVTWAAFGFALLSFVFFLVNV
	'Escherichia coli YP_006125567.1'                        --------MSVLYPLIQALVLFAVAPLLSGITRVARARLHNRRGPGVLQEYRDIFKLLGRQSVGPDASG-WVFRLTPYVMVGVMLTIATALPVVTVGSPLPQLGDLITLLYLFAIARFFFAISGLDTGSPFTAIGASREAMLGVLVEPMLLLGLWVAAQVAGSTNISNITDTVYHWPLSQS-IPLVLALCACAFATFIEMGKLPFDLAEAEQELQEGPLSEYSGSGFGVMKWGISLKQLVVLQMFVGVFIPWGQMETFTAGGLLLALVIAIVKLVVGVLVIALFENSMARLRLDITPRITWAGFGFAFLAFVSLLAA-
	'Escherichia coli YP_006125371.1'                        MRQTLCDGYLVIFALAQAVILLMLTPLFTGISRQIRARMHSRRGPGIWQDYRDIHKLFKRQEVAPTSSG-LMFRLMPWVLISSMLVLAMALPLFITVSPFAGGGDLITLIYLLALFRFFFALSGLDTGSPFAGVGASRELTLGILVEPMLILSLLVLALIAGSTHIEMISNTLAMGWNSP--LTTVLALLACGFACFIEMGKIPFDVAEAEQELQEGPLTEYSGAGLALAKWGLGLKQVVMASLFVALFLSFGRAQELSLACLLTSLVVTLLKVLLIFVLASIAENTLARGRFLLIHHVTWLGFSLAALAWVFWLTGL

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  318;

END;

BEGIN NOTES;

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

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  318;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  318;
END;

BEGIN TREES;
	Title 'Trees from "hyfC.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		1 'Thermococcus onnurineus TON_1022',
[1] 		2 'Thermacetogenium phaeum YP_006921296.1',
[2] 		3 'Geobacillus thermoglucosidasius YP_004587923.1',
[3] 		4 Geobacillus_sp._Y4.1MC1_YP_003989191.1,
[4] 		5 'Moorella thermoacetica YP_431022.1',
[5] 		6 'Thermoanaerobacter sp. YS13 THYS13_RS04685',
[6] 		7 'Caldanaerobacter subterraneus pacificus_CDSM653_01585',
[7] 		8 'Caldanaerobacter subterraneus tengcongensis_NP_623301.1',
[8] 		9 'Caldanaerobacter subterraneus yonseiensis_ERM92233.1',
[9] 		10 'Escherichia coli YP_006125567.1',
[10] 		11 'Escherichia coli YP_006125371.1';
	TREE tree_1 = ((((((6:0.014021,(8:0.000001,7:0.000001)0.730000:0.003476)0.732000:0.003867,9:0.01032)1.000000:0.139675,(5:0.082403,2:0.457843)0.740000:0.039928)0.964000:0.102146,(4:0.003457,3:0.000001)0.966000:0.09735)0.521000:0.153155,1:1.646428)0.915000:0.205499,11:0.397489,10:0.497788)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440387620353;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 5137850140701323610;
			tell It;
				setSelected  1;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 5833290321610925417;
			mqVersion 304;
			checksumv 0 3 3509409659 null  getNumChars 318 numChars 318 getNumTaxa 11 numTaxa 11   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 3.3542404409369E13 sumSquares 3.3542404409369E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1 errorReportedDuringRun;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 234;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 1315 683;
			setLocation 51 24;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #5137850140701323610 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #5137850140701323610;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1081 611;
					setLocation 51 24;
					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 #5137850140701323610  #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
			tell It;
				suppressEPCResponse;
				setTreeSource  #mesquite.trees.StoredTrees.StoredTrees;
				tell It;
					setTreeBlock 1;
					toggleUseWeights off;
				endTell;
				setAssignedID 4326.1440387279454.5817612514864147944;
				getTreeWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1081 611;
					setLocation 51 24;
					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 '((((((6:0.014021,(8:0.000001,7:0.000001)0.730000:0.003476)0.732000:0.003867,9:0.01032)1.000000:0.139675,(5:0.082403,2:0.457843)0.740000:0.039928)0.964000:0.102146,(4:0.003457,3:0.000001)0.966000:0.09735)0.521000:0.153155,(11:0.397489,10:0.497788)root:0.205499)0.915000:0.823214,1:0.823214);';
					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 #5833290321610925417 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 1081 611;
					setLocation 51 24;
					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;