#NEXUS [written Wed Aug 26 01:16:35 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 'Caldanaerobacter subterraneus pacificus_CDSM653_0106' 'Caldanaerobacter subterraneus tengcongensis_NP_621828.1' 'Caldanaerobacter subterraneus yonseiensis_ERM91339.1' 'Thermoanaerobacter ethanolicus WP_003868942.1' 'Thermoanaerobacter WP_004399986.1' 'Thermoanaerobacter wiegelii YP_004818933.1' 'Thermoanaerobacter italicus YP_003477425.1' 'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1' 'Thermoanaerobacterium saccharolyticum YP_006391303.1' 'Thermoanaerobacterium xylanolyticum YP_004469846.1' 'Thermoanaerobacterium thermosaccharolyticum YP_003850795.1' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=721; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX 'Caldanaerobacter subterraneus pacificus_CDSM653_0106' ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKET-----------------------------------------------------------------------------------------------------------------------------------------------KASAEKE-------EKEGI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Caldanaerobacter subterraneus tengcongensis_NP_621828.1' ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKET-----------------------------------------------------------------------------------------------------------------------------------------------KASAEKE-------EKEGI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Caldanaerobacter subterraneus yonseiensis_ERM91339.1' ----------------MLSMLKNVVYNLTHKPATRRYPF-EKRE---PFEGTRGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWKFEPFACIVCGACVDACPTKSLIM----------------------------------------------------------------------------------------------------------------------------------------LKEYRP-ISHEKYVIVQKKEV-----------------------------------------------------------------------------------------------------------------------------------------------KAPTEKE-------EKEGI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter ethanolicus WP_003868942.1' ----------------MLDMLKNVVSNLTHKPATRKYPF-EKRE---PFERARGHIE-NDIEKCILCGICQRVCPSNCIQVDRKE----GTWGFEPFACIICGVCVDACPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------LREYRP-ISNDKYVVLQKKEV-----------------------------------------------------------------------------------------------------------------------------------------------KNPPEKD-------KKEGI---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter WP_004399986.1' ----------------MLDMLKNVVSNLTHKPVTRKYPF-EKRE---PFEKARGHIE-NDIDKCILCGICQRVCPSNCIQVNRKE----GTWAFQPFECIICGVCVESCPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------AKEYRP-ISNEKYEIVQKKEV-------------------------------------------------------------------------------------------------------------------------Q---------------------NPPNKDK-------KEGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter wiegelii YP_004818933.1' ----------------MLDMLKNVVSNLTHKPVTRKYPF-EKRE---PFEKARGHIK-NDIDKCILCGICQRVCPSNCIQVNRKE----GTWAFQPFECIICGVCVESCPTKSLTM----------------------------------------------------------------------------------------------------------------------------------------AKEYRP-ISNEKYEIVQKKEV-------------------------------------------------------------------------------------------------------------------------Q---------------------NPPNKDK-------KEGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacter italicus YP_003477425.1' ----------------MLDMLKNVLSNLIHKPVTRKYPF-EKRE---PFERARGHIK-NDIDKCILCGICQRVCPSNCIQVNRKE----GKWVFQPFECVICGACVENCPTKSLKM----------------------------------------------------------------------------------------------------------------------------------------EAEYRA-VSNEKYEIVHKKEV-------------------------------------------------------------------------------------------------------------------------K---------------------NPPTKDK-------KEVA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1' ----------------MLDMLKSVFSNLSKKPATRMYPF-VERK---PFDINRGHLE-NDIEKCIFCSMCQRVCPSNCIKVDRKN----GVWEYDPFECVICGVCVEKCPKKCLRL----------------------------------------------------------------------------------------------------------------------------------------DTHYRS-CTDKKYDVHLERHE-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium saccharolyticum YP_006391303.1' ----------------MLDMLKSVFSNLSKKPVTRMYPF-EERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCIKVDRKT----GVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium xylanolyticum YP_004469846.1' ----------------MLDMLKNVFSNLSKKPVTRMYPF-EERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCISVDRKT----SVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Thermoanaerobacterium thermosaccharolyticum YP_003850795.1' ----------------MLDMLKSVFSNLSRKPVTRMYPF-VERK---PFDINRGHLE-NNIDECIFCGMCQRVCPSNCIKVDRKT----SVWEYNPFECVLCGVCVEKCPKKCLKL----------------------------------------------------------------------------------------------------------------------------------------DVHYRS-CTDKKYNIHLEKHD-----------------------------------------------------------------------------------------------------------------------------------------------DSEKAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 721; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 11; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 721; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 721; END; BEGIN TREES; Title 'Trees from "echF.tre"'; LINK Taxa = Taxa; TRANSLATE [0] n0 'Caldanaerobacter subterraneus pacificus_CDSM653_0106', [1] n1 'Caldanaerobacter subterraneus tengcongensis_NP_621828.1', [2] n2 'Caldanaerobacter subterraneus yonseiensis_ERM91339.1', [3] n3 'Thermoanaerobacter ethanolicus WP_003868942.1', [4] n4 'Thermoanaerobacter WP_004399986.1', [5] n5 'Thermoanaerobacter wiegelii YP_004818933.1', [6] n6 'Thermoanaerobacter italicus YP_003477425.1', [7] n7 'Thermoanaerobacterium thermosaccharolyticum YP_007297553.1', [8] n8 'Thermoanaerobacterium saccharolyticum YP_006391303.1', [9] n9 'Thermoanaerobacterium xylanolyticum YP_004469846.1', [10] n10 'Thermoanaerobacterium thermosaccharolyticum YP_003850795.1'; TREE tree_1 = ((((n10:0.009577,n9:0.019778)0.7850:0.009896,n8:0.000001)0.9580:0.084827,n7:0.01935)1.0000:0.305725,(((n2:0.000001,(n1:0.000001,n0:0.000001)0.0000:0.000001)0.9920:0.109235,n3:0.027611)0.4820:0.034472,(n4:0.000001,(n5:0.000001,n6:0.115544)0.8300:0.009615)0.8690:0.05456)0.9540:0.140674)root; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1440562595889; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4701866351056625355; tell It; setDefaultOrder 6 5 4 7 8 9 10 3 2 1 0; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3579119008059615784; mqVersion 304; checksumv 0 3 395746734 null getNumChars 721 numChars 721 getNumTaxa 11 numTaxa 11 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.3762323386455E13 sumSquares 1.3762323386455E13 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 1315 683; setLocation 51 -4; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4701866351056625355 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4701866351056625355; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1081 611; setLocation 51 -4; 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 #4701866351056625355 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 3134.1440562580531.6695088476363218836; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1081 611; setLocation 51 -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; 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 #3579119008059615784 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1081 611; setLocation 51 -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;