#NEXUS [written Tue Aug 25 00:25:12 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=7; TAXLABELS 'Caldanaerobacter subterraneus yonseiensis_ERM91260.1' Thermoanaerobacter_siderophilus_EIW00259.1 Thermoanaerobacter_ethanolicus_EGD52030.1 'Thermoanaerobacter wiegelii YP_004818844.1' Thermoanaerobacter_thermohydrosulfuricus_EMT39655.1 'Caloramator australicus WP_008908963.1' 'Thermobrachium celere WP_018663225.1' ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=162; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX 'Caldanaerobacter subterraneus yonseiensis_ERM91260.1' MALGDKSVYSPLTNLKNLFKKPMTVKYPKEILKVFPKDGVSPIYRGLHTNDLTKCIGCGMCQRICPFDAIEMKVVGENEQGRAIKKPVVDYGRCSFCGFCVDVCPTNSLKMSRHYIYKVKTVKSMSAKEEVEHIKQKFKLMPDESLGDDIGYNTGKTKKILG Thermoanaerobacter_siderophilus_EIW00259.1 MALGDKSVYSPLTNLKNLFKKPMTVKYPKEILKVFPKDGVSPIYRGLHTNDLTKCIGCGMCQRICPFDAIEMKVVSENEQGRAIKKPVVDYGRCSFCGFCVDVCPTNSLKMSRHYIYKVKTVKSMSAKEEVEHIKQKFKLMPDESLGDDIGYNTGKTKKILG Thermoanaerobacter_ethanolicus_EGD52030.1 MSLGDKSVYSPLTNLKNLFKKPMTVKYPKEILKVFPKDGVSPIYRGLHTNDLNKCIGCGMCQRICPFDAIEMKVIGENEQGRAIKKPVVDYGRCSFCGFCVDVCPTNSLKMSRHYIYKVKTVKSMSAKEEVEHIKQKFKLLPDESLGDDIGYNTGKTKKILG 'Thermoanaerobacter wiegelii YP_004818844.1' MSLGDKSVYSPLTNLKNLFKKPMTVKYPKEILKVFPKDGVSPIYRGLHTNDLNKCIGCGMCQRICPFDAIEMKVIGENEQGRAIKKPVVDYGRCSFCGFCVDVCPTNSLKMSRHYIYKVKTVKSMSAKEEVEHIKQKFKLMPDESLGDDIGYNTGKAKKILG Thermoanaerobacter_thermohydrosulfuricus_EMT39655.1 MSLGDKSVYSPLTNLKNLFKKPITVKYPKEILKVFPKDGVSPIYRGLHTNDLNKCIGCGMCQRICPFDAIEMKVIGENEQGRAIKKPVVDYGRCSFCGFCVDVCPTNSLKMSRHYIYKVKTVKSMSAKEEVEHIKQKFKLMPDESLGDDIGYNTGKAKKILG 'Caloramator australicus WP_008908963.1' MALGDKSVYSPLTTLKNLFKRPMTIKYPKEILRVFPKEGVSPNYRGLHTNDLEKCVGCAACQRICPFDAIEMKIIGQNEQGRAIKKPVVDYGRCSFCAFCVDVCPTNSLKMSRHYIYKIKTVKSLSAKDEVEFVKDKFRIMPDEKLGDDIGYNTGKAKKVLG 'Thermobrachium celere WP_018663225.1' MALGDKSVYSPLTTLKNLFRRPVTIKYPKQILRVFPKDGVSPTYRGLHTNDLDKCVGCAACKRICPFDAITMKVVGKNEQGREIKKPVVDYGRCSFCAFCVDVCPTNSLKMSRHYIYKIKTVMSMSAKDEVEYVKEKFKIMPDESLGDDIGYNTGKSKKVLG ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 162; END; BEGIN NOTES; TAXABITS TAXA = Taxa NAME = newlyAddedTaxon on = 1 - 7; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 162; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 162; END; BEGIN TREES; Title 'Trees from "MbxN.tre"'; LINK Taxa = Taxa; TRANSLATE [0] n0 'Caldanaerobacter subterraneus yonseiensis_ERM91260.1', [1] n1 Thermoanaerobacter_siderophilus_EIW00259.1, [2] n2 Thermoanaerobacter_ethanolicus_EGD52030.1, [3] n3 'Thermoanaerobacter wiegelii YP_004818844.1', [4] n4 Thermoanaerobacter_thermohydrosulfuricus_EMT39655.1, [5] n5 'Caloramator australicus WP_008908963.1', [6] n6 'Thermobrachium celere WP_018663225.1'; TREE tree_1 = (((n4:0.006109,n3:0.000001)0.0000:0.000001,(n2:0.006137,(n1:0.006123,n0:0.000001)0.9340:0.018598)0.3980:0.006119)1.0000:0.0861345,(n6:0.07494,n5:0.055627)1.0000:0.0420345)root; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1440473112272; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6121053467317892853; tell It; setDefaultOrder 4 3 2 1 0 6 5; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4814037165678359928; mqVersion 304; checksumv 0 3 2849434553 null getNumChars 162 numChars 162 getNumTaxa 7 numTaxa 7 short false bits 786431 states 786431 sumSquaresStatesOnly 1.5577555289505E13 sumSquares 1.5577555289505E13 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 #6121053467317892853 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6121053467317892853; 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; 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 #6121053467317892853 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1769.1440473103603.2704075303291826954; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 466 392; setLocation 51 24; 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 #4814037165678359928 #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;