#NEXUS [written Mon Aug 24 13:21:35 BRT 2015 by Mesquite version 3.04 (build 725) at fernando-To-be-filled-by-O-E-M/127.0.1.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=9; TAXLABELS 'Caldanaerobacter subterraneus pacificus_CDSM653_01583' 'Caldanaerobacter subterraneus yonseiensis_ERM92231.1' 'Geobacillus sp. Y4.1MC1 YP_003989193.1' 'Geobacillus thermoglucosidasius YP_004587925.1' 'Moorella thermoacetica YP_431020.1' 'Thermacetogenium phaeum YP_006921298.1' 'Caldanaerobacter subterraneus tengcongensis_NP_623299.1' 'Thermoanaerobacter YS13 THYS13_RS04660 ' 'Escherichia coli YP_006125374.1' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=529; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX 'Caldanaerobacter subterraneus pacificus_CDSM653_01583' VIEVEKSILFYLLLAVPLATSFLAF-----GIKSRRVVEAVHFAGISIEAFLSLQMVQYVIREERLFALGDMLYADSLVAILLLIIGVVGFLNGFYSIGHMRYDISRGEIDEKEISSYYSFYHILLFTMVLCALSNNIAIMWVALEATTLGSAFLVGFYKHKASAEAAWKYVLICSVGLAFALYGTILTYSNAFAMVQDAHKAMLWTELIKMAPRLDQQVMKLAFVFILIGFGTKVGLVPMHTWLPDTYSESPSPVSALLSGVLMKCALFAIIKYYTIALQAIGKEFLETLLLIFGLVSVGVSAFFILVQKDIKRKLAYSSVEHVGIIATGLGVGGTFGVLGALLHAINHSVTKSLLFCTAGNVIVKYGTRDSQRIRGIFKVAPVTAFLWTAGLLALVGSPPFNIFISEVVTVIAGIEAGHFWAMILFLVLLVVVFVAFFVLISETVIGSPPEDLPKGDVNWLTLLPIGILFVFMAALGLHLPSTLSQLLQRAVTIVLGGTI--------------------------- 'Caldanaerobacter subterraneus yonseiensis_ERM92231.1' ---MEKSILFYLLLAVPLATSFLAF-----GIKSRRLVEAVHFAGISIEAFLSLQMVQYVIREERLFALGDMLYADSLVAILLLIIGVVGFLNGFYSIGHMRYDISRGEIDEKEISSYYGFYHILLFTMVLCALSNNIAIMWVALEATTLSSAFLVGFYKHKASAEAAWKYVLICSVGLAFALYGTILTYSNAFAMVQDAHKAMLWTELIKMAPRLDQQVMKLAFVFILIGFGTKVGLVPMHTWLPDTYSESPSPVSALLSGVLMKCALFAIIKYYTIALQAIGKEFLETLLLIFGLVSVGISAFFILVQKDIKRKLAYSSVEHVGIIATGLGVGGTFGVLGALLHAINHSVTKSLLFCTAGNVIVKYGTRDSQKIRGIFKVAPITAFLWTAGLLALVGSPPFNIFISEVVTVIAGIEAGHFWAMILFLVLLVVVFVAFFVLISETVVGSPPEDLPKGDVNWLTLLPIGILFVFMVALGLHLPSTLSQLLQRAVTIVLGGTI--------------------------- 'Geobacillus sp. Y4.1MC1 YP_003989193.1' MIEMGENILIY-LPAVPLGTALLAF-----AIRSRRMVETVHFLGISILALLSLLLVKSVLDGQSLFALDGMLFADELTAILILLIGVIGFLNGFYSIGYMRHELTHGEENEKGVCFYYGFYHIFLFTMVISAISNNIAIMWVAVEATTLGSAFLVGFYKHKTSAEGAWKYVLICSVGLAFALYGTILTYSNAFSSVQDAHRAMLWTELVRMGQDLDPQLMKLAFVFVLIGFGTKAGLFPMHTWLPDAHSEAPSPASALLSGVLLKCALFAIVRYYAIALQVVGKEFPNSLLLIFGLLTVGVAAFFILMQNDIKRKLAYSSVEHVGIIATGLGIGGALGIFASLLHTINHSITKSLLFCTTGNIMMKYGTRDANKIRGMLKVMPFTALMFMAGIIAVAGSPPFNIFVSEFTTLTAGLKSGHFWAMILFLLFLVIAFVALVLLISETVFGPPSEDLPRGDANWLTLLPFGILFVFMAWLGLYLPDPLNQLLQGAVSVVLGDK---------------------------- 'Geobacillus thermoglucosidasius YP_004587925.1' MIEMGENILIY-LPAVPLGTALLAF-----AIRSRRMVETVHFLGISILALLSLLLVKSVLDGQSLFALDGMLFADELTAILILLIGVIGFLNGFYSIGYMRHELTHGEENEKGVCFYYGFYHIFLFTMVISAISNNIAIMWVAVEATTLGSAFLVGFYKHKTSAEGAWKYVLICSVGLAFALYGTILTYSNAFSSVQDAHRAMLWTELVRMGQDLDPQLMKLAFVFVLIGFGTKAGLFPMHTWLPDAHSEAPSPASALLSGVLLKCALFAIVRYYAIALQVVGKEFPNSLLLIFGLLTVGVAAFFILMQNDIKRKLAYSSVEHVGIIATGLGIGGALGIFASLLHTINHSITKSLLFCTTGNIMMKYGTRDANKIRGMLKVMPFTALMFMAGIIAVAGSPPFNIFVSEFTTLTAGLKSGHFWAMILFLLFLVIAFVALVLLISETVFGPPSEDLPRGDANWLTLLPFGILFVFMAWLGLYLPDPLNQLLQGAVSVVLGDK---------------------------- 'Moorella thermoacetica YP_431020.1' MIGVGENILFY-LPAVPLGIAVLAF-----GIRSRRIVELLHLAGITIVAFLSLLLVRSVLRGQTLFALNQMLYADSLTAILVLIIGVLGFLDGFYSIGYLRHDLEHGEADERSVCSYYGFFHIFLFTMLLSAISNNIAIMWAAVEATTLGSAFLVGFYKYKTSAEGAWKYVLICSVGLAFALYGTILTYSDAFTILQDAHRAMLWTEIAGMAHSLDPQVMKLAFVFILLGFGTKAGLFPMHTWLPDAHSEAPSPASAMLSGVLLKCALFAIIRYYAIALQVLGRSFPQTLLLIFGLLSVCVAAFFILVQNDIKRKLAYSSVEHIGIITTGLGVGGALGIFAALLHAINHSITKSLLFCASGNVVIKYGTRDSQKIRGLLKVAPFTGLMFMAGLLTVAGSPPLNIFVSEFMTLTAGLKGGYLWPMILLLIALVIVFAALVILISGSVFGSPPEGLSRGEVGWLTLLPFGILFLLMAGLGIYIPAPLNQLLQSAVNVVLGAR---------------------------- 'Thermacetogenium phaeum YP_006921298.1' ---MDENILIW-LLAFPLALSLITFLIRAVGWRSQRVPEVLHLGGIIIVLALILKTAFLIYSGGELSALADLFYADRLTAVFLLVIGVMGFLNGLYSIGYLRYDLAGEELGVDSCSTYYGFFHLFLFTMLFTVLSNNIALMWVGIEATTLGSVFLVGIYGRRESLEAAWKYILICSVGIAFALYGTILIYAGSFNLLQNAHNSMLWTEVVKSAGMLDPQVVKLAFVFILIGFGTKAGLFPMHTWLPDAHSEAPSPVSSLLSGVLLKCALFAIIKYYMIAARCLGPDFPRLLLLIFGILSIACAAFLIFAQRDLKRMFAYSSIENIGIIAIGLGIGGPLGVFAALLHTINHSITKSLLFCTSGNILIKYGTRDLKAIKGVFRAAPLTAFFLGSGALGIAGCPPLNIFISKLLTVSAGIQAGYLWPMLLCLALLVVVFASFLRLIGETLFGEPPEGMEKGDVNWITLLPIALLFLLMLALGVHTPEPLAELLEGAASLVTGI----------------------------- 'Caldanaerobacter subterraneus tengcongensis_NP_623299.1' ---MEKSILFYLLLAVPLATSFLAF-----GIKSRRVVEAVHFAGISIEAFLSLQMVQYVIREERLFALGDMLYADSLVAILLLIIGVVGFLNGFYSIGHMRYDISRGEIDEKEISSYYGFYHILLFTMVLCALSNNIAIMWVALEATTLGSAFLVGFYKHKASAEAAWKYVLICSVGLAFALYGTILTYSNAFAMVQDAHKAMLWTELIKMAPRLDQQVMKLAFVFILIGFGTKVGLVPMHTWLPDTYSESPSPVSALLSGVLMKCALFAIIKYYTIALQAIGKEFLETLLLIFGLVSVGVSAFFILVQKDIKRKLAYSSVEHVGIIATGLGVGGTFGVLGALLHAINHSVTKSLLFCTAGNVIVKYGTRDSQRIRGIFKVAPVTAFLWTAGLLALVGSPPFNIFISEVVTVIAGIEAGHFWAMILFLVLLVVVFVAFFVLISETVIGSPPEDLPKGDVNWLTLLPIGILFVFMAALGLHLPSTLSQLLQRAVTIVLGGTI--------------------------- 'Thermoanaerobacter YS13 THYS13_RS04660 ' ----------------------------------------------------------------------------------------------------------NSEIDEKEISSYYGFYHIFLFTMVLCALSNNIAIMWVALEATTLCSAFLVGLYKHKASAEAAWKYVLICSVGLAFALYGTILTYSNAFAMVQDAHKAMLWTELIKMAPRLDQQVMKLAFVFILIGFGTKVGLVPMHTWLPDTYSESPSPVSALLSGVLIECALFAIIKYYTIALQAIGKEFLETLLLIFGLVSVGVSAFFILVQKDIKRKLAYSSVEHVGIIATGLGVGGTFGVLGALLHAINHSVTKSLLFCTAGNVIVKYGTRDSQKIRGIFKVAPVTAFLWTAGLLALVGSPPFNIFISEVVTVIAGIEAGHFWAMILFLVLLVVVFVAFFVLISETVIGSPPEDLPKGDVNWLTLLPIGILFVFMAALGLHLPSTLSQLLQRAVTIVLGGTI--------------------------- 'Escherichia coli YP_006125374.1' ---MSYSVMFALLLLTPLLFSLLCFACRKRGLSATCTVTVLHSLGITLLLILALWVVQTAADAGEIFAAGLWLHIDGLGGLFLAILGVIGFLTGVYSIGYMRHEVAHGELSPVTLCDYYGFFHLFLFTMLLVVTSNNLIVMWAAIEATTLSSAFLVGIYGQRSSLEAAWKYIIICTVGVAFGLFGTVLVYANVASVMPQAEMAIFWSEVLKQSSLLDPTLMLLAFVFVLIGFGTKTGLFPMHAWLPDAHSEAPSPVSALLSAVLLNCALLVLIRYYIIICQAIGSDFPNRLLLIFGMLSVAVAAFFILVQRDIKRLLAYSSVENMGLVAVALGIGGPLGIFAALLHTLNHSLAKTLLFCGSGNVLLKYGTRDLNVVCGMLKIMPFTAVLFGGGALALAGMPPFNIFLSEFMTVTAGLARNHLLIIVLLLLLLTLVLAGLVRMAARVLMAKPPQAVNRGDLGWLTTSPMVILLVMMLAMGTHIPQPVIRILAGASTIVLSGTHDLPAQRSTWHDFLPSGTASVSEKHSER ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 529; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 9; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 529; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 529; END; BEGIN TREES; Title 'Trees from "hyfF.tre"'; LINK Taxa = Taxa; TRANSLATE [0] 1 'Caldanaerobacter subterraneus pacificus_CDSM653_01583', [1] 2 'Caldanaerobacter subterraneus yonseiensis_ERM92231.1', [2] 3 'Geobacillus sp. Y4.1MC1 YP_003989193.1', [3] 4 'Geobacillus thermoglucosidasius YP_004587925.1', [4] 5 'Moorella thermoacetica YP_431020.1', [5] 6 'Thermacetogenium phaeum YP_006921298.1', [6] 7 'Caldanaerobacter subterraneus tengcongensis_NP_623299.1', [7] 8 'Thermoanaerobacter YS13 THYS13_RS04660 ', [8] 9 'Escherichia coli YP_006125374.1'; TREE tree_1 = ((((8:0.014637,((7:0.000001,1:0.002588)0.764000:0.002659,2:0.012921)0.751000:0.003947)1.000000:0.172502,(6:0.280278,9:0.458475)0.995000:0.175521)0.170000:0.067712,5:0.139546)1.000000:0.116497,4:0.000001,3:0.000001)root; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1440433295288; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5089811780075732473; tell It; setDefaultOrder 2 3 8 7 6 4 1 0 5; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5483460514632503213; mqVersion 304; checksumv 0 3 1958950145 null getNumChars 529 numChars 529 getNumTaxa 9 numTaxa 9 short false bits 1048575 states 1048575 sumSquaresStatesOnly 5.002303322192E13 sumSquares 5.002303322192E13 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1873 995; setLocation 47 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #5089811780075732473 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #5089811780075732473; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1773 923; setLocation 47 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.arrow; 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 #5089811780075732473 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1754.1440433259803.3305251216989409876; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1773 923; setLocation 47 -4; 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 '((6:0.280278,((8:0.014637,((7:0.000001,1:0.002588)0.764000:0.002659,2:0.012921)0.751000:0.003947)1.000000:0.172502,(5:0.139546,(4:0.000001,3:0.000001)root:0.116497)1.000000:0.067712)0.170000:0.175521)0.995000:0.2292375,9:0.2292375);'; 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 #5483460514632503213 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1773 923; setLocation 47 -4; 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;