#NEXUS
[written Wed Aug 26 11:03:43 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=14;
	TAXLABELS
		'Caldanaerobacter subterraneus tengcongensis_NP_621834.1' 'Caldanaerobacter subterraneus pacificus_CDSM653_0112' 'Caldanaerobacter subterraneus yonseiensis_ERM91357.1' 'Caldanaerobacter subterraneus tengcongensis_3VTI' 'Thermoanaerobacter ethanolicus WP_003868948.1' 'Thermoanaerobacter italicus YP_003477419.1' 'Thermoanaerobacter siderophilus WP_006569909.1' 'Thermoanaerobacter WP_004399980.1' 'Thermoanaerobacter wiegelii YP_004818939.1' 'Thermoanaerobacter mathranii YP_003677315.1' 'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1' 'Thermoanaerobacterium xylanolyticum YP_004469852.1' 'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1' 'Thermoanaerobacterium saccharolyticum YP_006391309.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=386;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Caldanaerobacter subterraneus tengcongensis_NP_621834.1'   ------MHGVFGRVLCSVLQVWRIRGDLM-ERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
	'Caldanaerobacter subterraneus pacificus_CDSM653_0112'      -----------------------------MERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
	'Caldanaerobacter subterraneus yonseiensis_ERM91357.1'      -----------------------------MERVLLSHGGGGTMMEKLIEEVFADAFDNEYIRAMEDAALL---F---------------G--NLTFTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDGIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIERLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGLDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
	'Caldanaerobacter subterraneus tengcongensis_3VTI'          --------------------------------------------GALIEEVFADAFDNEYIRAMEDAALL---F---------------G--NITLTTDSFTVKPLFFPGGDIGKLAVCGTVNDASMRGAKPLFLTAAFIIEEGFPVEDLKKIVKSMAEAAKEAGVKIVAGDTKVVEKGSVDRIFINTSGIG-VLYEGA-NVSIKNAKPGDIVLISGTIGDHGMAVMSAREELQFDTPIFSDVAPLNGLIEKLMTLGEA-IKVLRDPTRGGVAEVLYEISKMSGVGIKIYEEKLPVKESVKSACEFMGIDFLHLANEGKVVVVVERDYAEKALEIMKSHEYGKDAEIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
	'Thermoanaerobacter ethanolicus WP_003868948.1'             -----------------------------MDKVLLSHGGGGTMMENLIEEVFSKAFDNEYIKGMEDAALL---F---------------G--NITLTTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIENLKRIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
	'Thermoanaerobacter italicus YP_003477419.1'                -----------------------------MDKVLLSHGGGGTMMESLIEEVFSKAFDNEYIKGMEDAALL---F---------------G--NITFTTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPMEDLKKIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFINTSGIG-VVYENV-DVSIKNAKPGDVVLVSGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKDSVKHACEMMGFDFLHLANEGKLITVIDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTINTIYGTSRIVDRPIGELLPRIC
	'Thermoanaerobacter siderophilus WP_006569909.1'            -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVEKGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
	'Thermoanaerobacter WP_004399980.1'                         -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVENGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
	'Thermoanaerobacter wiegelii YP_004818939.1'                -----------------------------MDKVLLSHGGGGTMMERLIEEVFAKAFDNEHINAMEDAALL---F---------------G--NIAITTDSFTVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPIEDLKRIVKSMAEAAEEAGVKIVAGDTKVVENGGIDGVFINTSGIG-VVYENV-DVSIKNARPGDVVLISGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKESVKSACDLMGFDFLHLANEGKLIAVVDRKYAEEALEIMKSDKYGKNAAIIGEVNDSK-----LVTINTVYGTSRIIDRPIGELLPRIC
	'Thermoanaerobacter mathranii YP_003677315.1'               -----------------------------MDKVLLSHGGGGTMMESLIEEVFSKAFDNEYIKGMEDAALLFE--------------------NITFTTDSFIVKPIFFPGGDIGRLAVCGTVNDASMRGAKPLYLTSAFIIEEGYPMEDLKRIVKSMAETAEEAGVKIVAGDTKVVEKGGVDGVFITTSGIG-VVYENV-DVSIKNAKPGDVVLVSGTIGDHGMAIMSAREELQFDPPILSDVSPLNKLIEKLMTLGKA-VKVLRDPTRGGVAEVLYEISKMSGVGIKIYEDKLPVKDSVKYACDMMGFDFLHLANEGKLIAVIDRKYAEEALEIMKSDKYGKDAAIIGEVNDSK-----LVTLNTIYGTSRIVDRPIGELLPRIC
	'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1' -----------------------------MDKILMTHGGGGSMMQSFIDEIFISKFDNQYIKEMEDAALL---P---------------G--KIVFTTDSFVVKPLFFPGGDIGRLSVCGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKRIVNSMEDTANEAGVQIVTGDTKVVEKNSADGVFINTAGIG-ILPDGA-DISIKNGKPGDVVIISGTIGDHGMAVMSAREEINFEPPLFSDVSPLNKMVEKLATLKSA-VKILRDPTRGGVAEVLYEIANMSNVGIKIYEDKLPVKESVKSACSMLGLDYLHLANEGKLVCVVERDYADEALKLMKEDIYGKDASIIGEIND--TG---LVTIETVYGTTRIVDRPLGELLPRIC
	'Thermoanaerobacterium xylanolyticum YP_004469852.1'        -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLNQMEDAALL---P---------------G--KTVFTTDSFVVKPVFFPGGDIGRLAICGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKKIVDSMVDAANEAGVQIVTGDTKVVEKNSADGIFINTAGIG-ILPDGA-YVSIKNGEPGDVVIVSGTIGDHGMAVMGAREGLDFDPPLFSDVSPLNKMVQKLMTLKDA-VKILRDPTRGGVAEVLYEIASMSNVGIKIHEDKLPVKESVKSACSMLGIDFLHLANEGKLICVVDKDFAYKALEIMKGDKYGKDAAIIGEI--DDSG---LVTIETVYGTNRIIDRPIGELLPRIC
	'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1' -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLSQMEDAALL---P---------------G--KTVFTTDSFVVKPLFFPGGDIGRLSVCGTVNDISMRGAKPLFLSASFIIEEGFPVDDIKRIVNSMEDTANEAGVQIVTGDTKVVEKNSADGIFINTAGIG-ILPDGA-SVSIKNGKPGDVVIVSGTIGDHGMAVMGAREGIDFDPPLLSDVSPLNKMVEKLMALRDA-VKILRDPTRGGVAEVLYEIAGMSNVGIKIYEDKLPVKENVKSACSMLGIDYLHLANEGKLVCVVDKDFAYKALEIMKDDKYGKDAAIIGEI--DDSG---LVTIETIYGTNRIVDRPIGELLPRIC
	'Thermoanaerobacterium saccharolyticum YP_006391309.1'      -----------------------------MDKVLMSHGGGGSMMQSFISEIFIEKFNNEYLSQMEDAALL---P---------------G--KTVFTTDSFVVKPIFFSGGDIGRLAICGTVNDISMRGAKPLFLSASFIIEEGFPIDDIKRIVDSMVDAANEAGVQIVTGDTKVVEKHSADGIFINTAGIG-ILHDEA-SVSIKNGKPGDAVIISGTIGDHGMAVMGDREGLDFEPPLLSDVSPLNKMVEKLMTLKDA-VKILRDPTRGGVAEVLYEIASMSNVGIKIYEDKLPVKESVKSACSMLGIDYLHLANEGKLVCVVDKDYAYKALEIMKDDKYGKDAAIIGEI--DDSG---LVTIETIYGTNRIVDRPIGELLPRIC

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  386;

END;

BEGIN NOTES;

	TAXABITS   TAXA = Taxa NAME = newlyAddedTaxon on =  1 -  14;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  386;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  386;
END;

BEGIN TREES;
	Title 'Trees from "hypE.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		n0 'Caldanaerobacter subterraneus tengcongensis_NP_621834.1',
[1] 		n1 'Caldanaerobacter subterraneus pacificus_CDSM653_0112',
[2] 		n2 'Caldanaerobacter subterraneus yonseiensis_ERM91357.1',
[3] 		n3 'Caldanaerobacter subterraneus tengcongensis_3VTI',
[4] 		n4 'Thermoanaerobacter ethanolicus WP_003868948.1',
[5] 		n5 'Thermoanaerobacter italicus YP_003477419.1',
[6] 		n6 'Thermoanaerobacter siderophilus WP_006569909.1',
[7] 		n7 'Thermoanaerobacter WP_004399980.1',
[8] 		n8 'Thermoanaerobacter wiegelii YP_004818939.1',
[9] 		n9 'Thermoanaerobacter mathranii YP_003677315.1',
[10] 		n10 'Thermoanaerobacterium thermosaccharolyticum YP_007297559.1',
[11] 		n11 'Thermoanaerobacterium xylanolyticum YP_004469852.1',
[12] 		n12 'Thermoanaerobacterium thermosaccharolyticum YP_003850801.1',
[13] 		n13 'Thermoanaerobacterium saccharolyticum YP_006391309.1';
	TREE tree_1 = ((((n13:0.031517,n11:0.042239)0.9400:0.025978,n12:0.011315)0.7340:0.054186,n10:0.061975)0.9910:0.136071,(((n9:0.013433,n5:0.011126)0.5280:0.0189,(((n8:0.000001,n7:0.003409)0.8380:0.003407,n6:0.000001)0.9900:0.031345,n4:0.004465)0.8510:0.023837)0.9800:0.074041,((n3:0.006911,(n1:0.000001,n0:0.000001)0.0000:0.000001)0.8900:0.010665,n2:0.006626)0.9790:0.076519)0.6010:0.0965)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440597823306;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 5196205874685653575;
			tell It;
				setDefaultOrder  12 11 13 10 9 5 8 7 6 4 3 1 2 0;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 4108662108802865763;
			mqVersion 304;
			checksumv 0 3 2213838138 null  getNumChars 386 numChars 386 getNumTaxa 14 numTaxa 14   short false   bits 1048575   states 1048575   sumSquaresStatesOnly 3.8300705538947E13 sumSquares 3.8300705538947E13 longCompressibleToShort false usingShortMatrix false   NumFiles 1 NumMatrices 1;
			mqVersion;
		endTell;
		getWindow;
		tell It;
			suppress;
			setResourcesState false false 234;
			setPopoutState 300;
			setExplanationSize 0;
			setAnnotationSize 0;
			setFontIncAnnot 0;
			setFontIncExp 0;
			setSize 700 583;
			setLocation 61 62;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #5196205874685653575 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #5196205874685653575;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 511;
					setLocation 61 62;
					setFont SanSerif;
					setFontSize 10;
					getToolPalette;
					tell It;
						setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam;
					endTell;
					setActive;
				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.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #4108662108802865763 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 511;
					setLocation 61 62;
					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;