#NEXUS
[written Wed Aug 26 11:15:49 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 pacificus_CDSM653_0107' 'Caldanaerobacter subterraneus tengcongensis_NP_621829.1' 'Caldanaerobacter subterraneus yonseiensis_ERM91340.1' 'Thermoanaerobacter italicus YP_003477424.1' 'Thermoanaerobacter mathranii YP_003677320.1' 'Thermoanaerobacter ethanolicus WP_003868943.1' 'Thermoanaerobacter wiegelii YP_004818934.1' 'Thermoanaerobacterium thermosaccharolyticum YP_007297554.1' 'Thermoanaerobacterium xylanolyticum YP_004469847.1' 'Thermoanaerobacterium saccharolyticum YP_006391304.1' 'Thermoanaerobacterium thermosaccharolyticum YP_003850796.1' 'Coprothermobacter platensis WP_018962511.1' 'environmental samples WP_022167113.1' 'Clostridium celatum WP_005210164.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=154;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Caldanaerobacter subterraneus pacificus_CDSM653_0107'      ------------------------------MLVEEAEKRKVKKVTKVTVVIGELTGIESESVKFYFDILT-ENTVAEGAELVFKIVRAQFKCTQCGNVFERSNFTFK---CPVCGGQ-GVLIDKRGKEFYIESIEVE-----------------
	'Caldanaerobacter subterraneus tengcongensis_NP_621829.1'   ------------------MHELSVTQGLVDMLVEEAEKRKVKKVTKVTVVIGELTGIESESVKFYFDILT-ENTVAEGAELVFKIVRAQFKCTQCGNVFERSNFTFK---CPVCGGQ-GVLIDKRGKEFYIESIEVE-----------------
	'Caldanaerobacter subterraneus yonseiensis_ERM91340.1'      ------------------MHELSVTQGLVDMLVEEAEKRKVKKVTKVTVVIGELTGIESESVKFYFDILT-ENTVAEGAELVFKIVRAQFKCTQCGNVFERSNFTFK---CPICGGQ-GVLIDKRGKEFYIESIEVE-----------------
	'Thermoanaerobacter italicus YP_003477424.1'                ------------------MHELSVTQSLVDMVLEEAQKREIKKVTKVTIVIGELTGLESESIQFYFGVLS-ENTVAEGAELVFKKIKAQFKCGQCGNIFERLNFTFN---CPVCGST-GVLVDK-GKEFYIESIEVE-----------------
	'Thermoanaerobacter mathranii YP_003677320.1'               ------------------MHELSVTQSLVDMVLEEAQKREIKKVTKVTIVIGELTGLESESIQFYFGVLS-ENTVAEGAELVFKKIKAQFKCGQCGNIFERVNFTFN---CPVCGST-GVLVDK-GKEFYIESIEVE-----------------
	'Thermoanaerobacter ethanolicus WP_003868943.1'             ------------------MHELSVTQSLVDMVLEEAEKREVKKVTKVTVVIGELTGLESESIKFYFDILS-ENTVAEGAELTFKIIKAQFKCRQCGTIFERSNFTFN---CPVCGGV-GVLVNK-GKEFYIESIEVE-----------------
	'Thermoanaerobacter wiegelii YP_004818934.1'                ------------------MHELSVTQSLVDILLEEAQKRNVKKVTKVTVVIGELTGLESESIRFYFDVLS-ENTVAEGAELVFKMIKAQFKCRQCGNIFERTNFTFN---CPVCGAT-GVLVDK-GKEFYIESIEVE-----------------
	'Thermoanaerobacterium thermosaccharolyticum YP_007297554.1' ------------------MHELSITESIVNMVSDEVKKRNINKVTKINIVLGELTGFEEDSIKFYFDVLS-EGTPLYGAELNFKRVKAEFKCRNCGMIYNRGNFTFK---CPYCGSS-GVLIEK-GKELYIDSIDVE-----------------
	'Thermoanaerobacterium xylanolyticum YP_004469847.1'        ------------------MHELSITESIVNMVSDEVKKRNVNKVTKINIVLGELTGFEEESIKFYFDVLS-EGTPLYGAKLDFKKVKAEFKCRSCGMIYNRGNFTFK---CPYCGSS-GVLIEK-GKELYIDSIDVE-----------------
	'Thermoanaerobacterium saccharolyticum YP_006391304.1'      ------------------MHELSITESIVNMVSDEAKKRNVNKVTKINIVLGELTGFEEESIRFYFEVLS-EGTPLYGAKLDFKKVKAEFKCRSCGMIYNRGNFTFK---CPYCGSS-GVLIEK-GKELYIDSIDVE-----------------
	'Thermoanaerobacterium thermosaccharolyticum YP_003850796.1' ------------------MHELSITESIVNMVSDEVKKRNINKVTKINIVLGELTGFEEDSIKFYFDVLS-EGTPLYGAILNFKRVKAEFKCRNCGMIYNRENFTFK---CPYCGSS-GVLIEK-GKELYIDSIDVE-----------------
	'Coprothermobacter platensis WP_018962511.1'                ------------------MHELSVTQSILDMAVEEAKKAGASSVDKISIVLGELTGIAEDCVRFYFDIIK-KDTLAENAQLSFSHVPAVLKCKKCGYEFERQTFSFT---CPKCGSP-GVLIDK-GKELYIDHIEVSFDGNKVGKEHT------
	'environmental samples WP_022167113.1'                      ------------------MHELSVTEGILKICLDEGKKHNIEKIKKINIVVGELTGLMPNCISYYFNIAA-KGTLAEDAEISIAYEKVMIKCHNCGFEGKFINKQYV---CPSCGKS-DYKIVK-GREFYIDTMEVE-----------------
	'Clostridium celatum WP_005210164.1'                        ------------------MHELAVTQSILKICIDEGEKYNVKRIKKLNIKVGELTDLVPSCISYYFKIVA-KDTIAEEAEINIEKIKVAITCNKCGYKGELGENNYV---CPKCKGN-NYKIIK-GREFYLDTMEVD-----------------

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  154;

END;

BEGIN NOTES;

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

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  154;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  154;
END;

BEGIN TREES;
	Title 'Trees from "hypA.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		n0 'Caldanaerobacter subterraneus pacificus_CDSM653_0107',
[1] 		n1 'Caldanaerobacter subterraneus tengcongensis_NP_621829.1',
[2] 		n2 'Caldanaerobacter subterraneus yonseiensis_ERM91340.1',
[3] 		n3 'Thermoanaerobacter italicus YP_003477424.1',
[4] 		n4 'Thermoanaerobacter mathranii YP_003677320.1',
[5] 		n5 'Thermoanaerobacter ethanolicus WP_003868943.1',
[6] 		n6 'Thermoanaerobacter wiegelii YP_004818934.1',
[7] 		n7 'Thermoanaerobacterium thermosaccharolyticum YP_007297554.1',
[8] 		n8 'Thermoanaerobacterium xylanolyticum YP_004469847.1',
[9] 		n9 'Thermoanaerobacterium saccharolyticum YP_006391304.1',
[10] 		n10 'Thermoanaerobacterium thermosaccharolyticum YP_003850796.1',
[11] 		n11 'Coprothermobacter platensis WP_018962511.1',
[12] 		n12 'environmental samples WP_022167113.1',
[13] 		n13 'Clostridium celatum WP_005210164.1';
	TREE tree_1 = (((((n6:0.04741,(n4:0.000001,n3:0.010251)0.9760:0.082985)0.8790:0.055839,n5:0.042898)0.8130:0.062964,(n2:0.010124,(n1:0.000001,n0:0.000001)0.0000:0.000001)0.9550:0.086751)0.9560:0.167472,(n9:0.017656,((n10:0.021928,n7:0.000001)0.9910:0.064142,n8:0.000001)0.3350:0.013908)0.9960:0.334218)0.8630:0.133974,((n13:0.337534,n12:0.170519)0.9990:0.626418,n11:0.316497)0.5430:0.178599)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440598549748;
		getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			setID 0 7620578925332442792;
			tell It;
				setDefaultOrder  6 5 4 2 1 3 0 9 10 7 8 13 12 11;
				attachments ;
			endTell;
		endTell;
		getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
		tell It;
			setID 0 3416106942341877429;
			mqVersion 304;
			checksumv 0 3 347198372 null  getNumChars 154 numChars 154 getNumTaxa 14 numTaxa 14   short false   bits 786431   states 786431   sumSquaresStatesOnly 1.701934490022E13 sumSquares 1.701934490022E13 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 700 464;
			setLocation 51 24;
			setFont SanSerif;
			setFontSize 10;
			getToolPalette;
			tell It;
			endTell;
			desuppress;
		endTell;
		getEmployee  #mesquite.minimal.ManageTaxa.ManageTaxa;
		tell It;
			showTaxa #7620578925332442792 #mesquite.lists.TaxonList.TaxonList;
			tell It;
				setTaxa #7620578925332442792;
				getWindow;
				tell It;
					newAssistant  #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 392;
					setLocation 51 24;
					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 #3416106942341877429 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
					setExplanationSize 30;
					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
					setSize 466 392;
					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;