#NEXUS
[written Wed Aug 26 10:57:53 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=13;
	TAXLABELS
		'Caldanaerobacter subterraneus pacificus_CDSM653_0111' 'Caldanaerobacter subterraneus tengcongensis_NP_621833.1' 'Caldanaerobacter subterraneus yonseiensis_ERM91343.1' 'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1' 'Thermoanaerobacter wiegelii YP_004818938.1' 'Thermoanaerobacter siderophilus WP_006569908.1' 'Thermoanaerobacter ethanolicus WP_003868947.1' 'Thermoanaerobacter mathranii YP_003677316.1' 'Thermoanaerobacter italicus YP_003477420.1' 'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1' 'Thermoanaerobacterium thermosaccharolyticum YP_003850800.1' 'Thermoanaerobacterium saccharolyticum YP_006391308.1' 'Thermoanaerobacterium xylanolyticum YP_004469851.1' 
	;

END;


BEGIN CHARACTERS;
	TITLE  Character_Matrix;
	DIMENSIONS  NCHAR=427;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	'Caldanaerobacter subterraneus pacificus_CDSM653_0111'      --------------------------------------------MQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEARERNIKNYSVYSLHKTMPEALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPVGDEIEIKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
	'Caldanaerobacter subterraneus tengcongensis_NP_621833.1'   -------------------------------------------MMQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEAKERKIKNYSVYSLHKTMPEALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPVGDEIEIKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
	'Caldanaerobacter subterraneus yonseiensis_ERM91343.1'      -------------------------------------------MMQ-QREIVE----KAKKAIETL----NPG--IPFNIMEVCGSHTMAISKFGLRQVLPKNIRLISGPGCPVCVTAQNEIDAVIELS--NKNIVIATFGDLIRVPGN-KS-SLQKERAKGKEVRVFYSPLDALKYAEENPQKEVVFIGIGFETTVPTVALTIKEARERNIKNYSVYSLHKTMPKALRALLVGGS-NVQGFLLPGHVSAITGSRIYEFLPREFGVGGVISGFEAEDILMSIVMLLKNYK---NPTIEIQYKRVVKEEGNIEAQKIIEEVFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIKPIGDEIEVKG---CRCGDVLKGRIYPNECPLFGRVCTPDNPVGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1'   -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVIELA--NKNVVIATFGDLIRVPGN-KS-SLQAERAAGKEVKVFYSPLDALKYAEENPSKEVVFIGIGFETTVPTVAVTIKEAREKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter wiegelii YP_004818938.1'                -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVIELA--NKNVVIATFGDLIRVPGN-RS-SLQAERAAGKEVKVFYSPLDALKYAEENPSKEVVFIGIGFETTVPTVAVTIKEAREKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter siderophilus WP_006569908.1'            -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GPFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVVELA--NRNVVIATFGDLIRVPGS-KS-SLQLERAAGKEVKVFYSPLDALKYAEGNPSKEVVFIGIGFETTVPTVAVTIKEAKEKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFIPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIEEIFEPCDSTWRGLGEIKGSGLKIRDKYKDFDAALKFDIRPIGEEIEIKG---CRCGDVLKGNIYPNECPLFGRVCTPENPAGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter ethanolicus WP_003868947.1'             -------------------------------------------MMQ-QTEMIE----KAKRAIEAL----NPG--GLFNIMEVCGSHTMAISKFGLRQLLPKNIRLISGPGCPVCVTAQNEIDSVVELA--NRNVVIATFGDLIRVPGS-KS-SLQLERAAGKEVKVFYSPLDALNYAEGNPSKEVVFIGIGFETTVPTVAVTIKEAKEKNIKNYSVYCLHKTMPEALRALLEGGS-NVQGFLLPGHVSAITGSKIYEFLPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NPAIEIQYKRVVRKEGNLEAQKIIDEIFEPCDSTWRGLGKIKGSGLRIKDKYKDFDAAVKFDIKPIGEEIKIKG---CRCGDVLKGSIYPNECPLFGRACTPENPVGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter mathranii YP_003677316.1'               --------------------------------------------MQ-QTEMIK----KAKEIIDVF----NPG--VQFNIMEVCGSHTMAISKFGLRQILPKNIRLISGPGCPVCVTAQNEIDSIIELS--NKNVVIATFGDLIRVPGS-KS-SLQQQRAAGKEIKVFYSPLDALKYAEENTTKEVVFIGIGFETTIPTVAVTIKEAKEKNIKNYSVYCLHKTMPETLRALLEGGS-NVQGFLLPGHVSAITGSKIYEFIPKEFGVSGVISGFEAMDILMSIIMLLKNYK---NSSIEIQYKRVVRKEGNIKAQKIIEEIFEPCDSTWRGLGKIKGSGLRIKDKYKDFDAAVKFDIKPIGGEIEIKG---CRCGDVLKGSIYPNECPLFGKACTPENPVGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacter italicus YP_003477420.1'                --------------------------------------------MQ-QTEMIK----KAKEIIDVF----NPG--VQFNIMEVCGSHTMAISKFGLRQILPKNIRLISGPGCPVCVTAQNEIDSIIELS--NKNVVIATFGDLIRVPGS-KS-SLQQQRAAGKEIKVFYSPLDALKYAEENPTKEVVFLGIGFETTIPTVAVTIKEAKKKNIKNYSVYCLHKTMPEALRVLLEEGS-KVQGFLLPGHVSAITGSKIYEFIPKEFGVGGVISGFEAMDILMSIIMLLKNYK---NSSIEIQYKRVVREEGNVKAQKIIEEIFEPCDSTWRGLGKIKGSGLKMKDKYKDFDAAVKFDIKPIGEEFEIKG---CRCGDVLKGSIYPNECPLFGNVCTPENPVGPCMVSSEGSCAAFYKYGA---------
	'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1' -----------------------------------------------MQDIIN----TAKKLIDKY----NIG--EPIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDAVISLA--GKGMTIATFGDLIRVPGN-NS-SLQEERAKGKDVKVFYSPIDALEYAKANTSKEVVFIGIGFETTIPSVALTIKEAHAKKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVSAITGSNIYNFLVDKYKIGGVVSGFEAQDILMSVVMILKNMK---NPKIEIQYKRVVREEGNADAKKLIEEVFEDSDATWRGLGMIEGSGLKIRDLYSEYDAEKKFHIQKPSEQIEING---CRCGDVLMGIISPHQCPLFGKACTPVNPIGPCMVSSEGSCAAYYKYGA---------
	'Thermoanaerobacterium thermosaccharolyticum YP_003850800.1' -----------------------------------------------MQDIIK----SARKLIDKY----NSG--EPIKIMEVCGSHTMAISRYGLRQILPENIKLISGPGCPVCVTAQNEIDAVISLA--GQGITIATFGDLIRVPGN-NS-SLQEERAKGKDVKVFYSPLDALEYAEANPSKEVVFIGIGFETTIPSVALTIKEAYTKKIKNYSVYCLHKTMPKALEALVINGS-DIQGFLLPGHVSAITGSTIYNFLVDKYKIGGVVSGFEAQDILISIIMILKNME---NPKIEIQYKRVVREEGNTDAKKLIEEVFEDSDATWRGLGMIEGSGLKIRDLYSEYDAEKKFHIQKPSEQIEING---CRCGDVLMGIISPHQCPLFGKACTPVNPIGPCMVSSEGSCAAYYKYGE---------
	'Thermoanaerobacterium saccharolyticum YP_006391308.1'      -----------------------------------------------MQGIIN----RAKELIDRY----NTG--EFIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDASISLA--SQGVTIATFGDLVRVPGN-DS-SLQEERAKGKDVRVFYSPLDALDYAMANPSKEVVFIGIGFETTIPSVAMTIKEAYTRKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVSAITGSSIYGFLVDKYKIGGVVSGFEATDILMSVVMILKNLK---DPKIEIQYKRVVKEGGNTEAQRLMDEIFEESDAEWRGLGMIEGSGLKIREKYSEYDAEKKFNIKKPNSRTEIKG---CRCGDVLKGLITPKQCPLFGKACTPLNPVGPCMVSSEGSCAAYYKYGE---------
	'Thermoanaerobacterium xylanolyticum YP_004469851.1'        -----------------------------------------------MQGIIN----TAKELIDRY----NIG--ESIKIMEVCGSHTMAISKYGLRQILPPNIKLISGPGCPVCVTAQNEIDASISLA--SQGVTIATFGDLVRVPGN-NS-SLQEERAKGRNVRVFYSPLDALDYAIANPSKEVVFIGIGFETTIPSVALTIKEAYTKKIKNYSVYCLHKTMPKALEALVVNGS-DIQGFLLPGHVAAITGSTIYNFLVDKYKIGGVVSGFEASDILMSVVMILKNLR---DPKIEIQYKRVVKEEGNTDAQSLIEEVFEESDAEWRGLGMIEGSGLKIREKYSEYDAEKKFNIKKPNSSTEIKG---CRCGDVLKGIITPKQCPLFGKACTPLNPVGPCMVSSEGSCAAYYKYGE---------

;


END;

BEGIN ASSUMPTIONS;
	TYPESET * UNTITLED   =  unord:  1 -  427;

END;

BEGIN NOTES;

	TAXABITS   TAXA = Taxa NAME = newlyAddedTaxon on =  1 -  13;

END;

BEGIN CODONS;
	CODESET * UNTITLED   =  universal:  1 -  427;


END;

BEGIN MESQUITECHARMODELS;
	ProbModelSet * UNTITLED   =  'Mk1 (est.)':  1 -  427;
END;

BEGIN TREES;
	Title 'Trees from "hypD.tre"';
	LINK Taxa = Taxa;
	TRANSLATE
[0] 		n0 'Caldanaerobacter subterraneus pacificus_CDSM653_0111',
[1] 		n1 'Caldanaerobacter subterraneus tengcongensis_NP_621833.1',
[2] 		n2 'Caldanaerobacter subterraneus yonseiensis_ERM91343.1',
[3] 		n3 'Thermoanaerobacter thermohydrosulfuricus WP_004399981.1',
[4] 		n4 'Thermoanaerobacter wiegelii YP_004818938.1',
[5] 		n5 'Thermoanaerobacter siderophilus WP_006569908.1',
[6] 		n6 'Thermoanaerobacter ethanolicus WP_003868947.1',
[7] 		n7 'Thermoanaerobacter mathranii YP_003677316.1',
[8] 		n8 'Thermoanaerobacter italicus YP_003477420.1',
[9] 		n9 'Thermoanaerobacterium thermosaccharolyticum YP_007297558.1',
[10] 		n10 'Thermoanaerobacterium thermosaccharolyticum YP_003850800.1',
[11] 		n11 'Thermoanaerobacterium saccharolyticum YP_006391308.1',
[12] 		n12 'Thermoanaerobacterium xylanolyticum YP_004469851.1';
	TREE tree_1 = (((n12:0.016796,n11:0.034917)0.9840:0.053301,(n10:0.018305,n9:0.023577)0.9450:0.033068)1.0000:0.159863,(((n8:0.025521,n7:0.016937)0.9990:0.060029,((n4:0.002614,n3:0.000001)0.0000:0.000001,(n5:0.002524,n6:0.029756)0.7690:0.016163)0.6210:0.020392)0.8530:0.027171,((n2:0.005247,n0:0.000001)0.0000:0.000001,n1:0.00525)0.9190:0.037643)0.9190:0.072549)root;

END;


Begin MESQUITE;
		MESQUITESCRIPTVERSION 2;
		TITLE AUTO;
		tell ProjectCoordinator;
		timeSaved 1440597473809;
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		tell It;
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			tell It;
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							setFixedTaxonDistance 0;
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				tell It;
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				tell It;
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				tell It;
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				endTell;
				getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings;
				tell It;
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				endTell;
				getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues;
				tell It;
					panelOpen false;
				endTell;
			endTell;
		endTell;
		getEmployee  #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
		tell It;
			showDataWindow #7082339191923918431 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
			tell It;
				getWindow;
				tell It;
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					setAnnotationSize 20;
					setFontIncAnnot 0;
					setFontIncExp 0;
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					setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
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				tell It;
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				endTell;
					colorRowNames  #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor;
					colorColumnNames  #mesquite.charMatrices.CharGroupColor.CharGroupColor;
					colorText  #mesquite.charMatrices.NoColor.NoColor;
					setBackground White;
					toggleShowNames on;
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					toggleColorsPanel off;
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				getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
				tell It;
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				endTell;
				getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
				tell It;
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				getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
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				getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
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				getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
				tell It;
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				getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip;
				tell It;
					showStrip off;
				endTell;
				getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
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					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;