#NEXUS [written Tue Jun 11 01:38:53 ART 2019 by Mesquite version 3.6 (build 917) at Nazareno-PC/192.168.56.1] BEGIN TAXA; TITLE Bacillus_spp.; DIMENSIONS NTAX=8; TAXLABELS A6_MH750312 Bacillus_amyloliquefaciens_DSM7_T_FN597644 Bacillus_velezensis_CR502_T_NZ_LHCC1000001 Bacillus_vallismortis_DSM_11031_T_NZ_JH600197 Bacillus_coagulans_NBRC_12583_T_CP009709 Bacillus_licheniformis_DSM_13_T_AE017333 Bacillus_methylotrophicus_CBMB_205_T_NZ_CP011937 Bacillus_subtilis_LMG_7135_T_CP015375 ; END; BEGIN CHARACTERS; TITLE recA_Bacillus_spp.; DIMENSIONS NCHAR=689; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX A6_MH750312 AAGGTTCCATCATGAAGCTCGGAGAAAAAACGGATACAAGAATTTCAACGGTGCCAAGCGGTTCCCTTGCACTTGATACCGCTCTCGGAATAGGCGGATACCCGCGCGGACGGATTATTGAAGTATACGGACCTGAAAGCTCAGGTAAAACGACTGTAGCGCTTCACGCAATCGCTGAGGTTCAGGAAAAAGGCGGACAGGCAGCATTTATTGATGCTGAGCATGCTCTTGATCCTGTTTACGCGCAAAAGCTCGGTGTCAATATCGAAGAGCTTCTGCTTTCTCAGCCGGATACGGGAGAGC---AGGCGCTAGAGATTGCAGAAGCGCTGGTGCGAAGCGGAGCGGTTG-ATATCGTAGTCGTTGACTCTGTTGCGGCGCTTGTTCCAAAAGCTGAAATTGACGGTGACATGGGTGATTCGCACGTCGGTTTACAAGCTCGTCTCATGTCTCAGGCGCTCCGTAAGCTTTCCGGCGCCATCAATAAATCTAAAACAATCGCAATCTTTATTAACCAGATTCGTGAAAAAGTCGGCGTTATGTTCGGAAATCCGGAGACGACACCGGGCGGCCGCGCGCTGAAA-TTCTATTCTTCCGTGCGCCT--TGAAGTGCGCCGTGCCGAG-CAATTAAAGCAGGGCAACGACGTCATGGGGAATAAA-ACGAGAATTAAAGTCGTAAAAAAC Bacillus_amyloliquefaciens_DSM7_T_FN597644 AAGGTTCCATCATGAAGCTCGGAGAAAAAACGGATACAAGAATTTCAACGGTGCCGAGCGGTTCCCTTGCACTTGATACCGCTCTCGGAATAGGCGGATACCCGCGCGGACGGATTATTGAAGTATACGGACCTGAAAGCTCAGGTAAAACGACTGTAGCGCTTCACGCAATCGCTGAGGTTCAGGAAAAAGGCGGACAGGCAGCATTTATTGATGCCGAGCATGCTCTTGATCCTGTGTACGCGCAAAAGCTCGGTGTCAATATCGAAGAGCTGCTGCTTTCTCAGCCGGATACGGGAGAGC---AGGCGCTGGAGATTGCTGAAGCGCTGGTGCGAAGCGGAGCTGTCG-ATATCGTAGTCGTTGACTCTGTTGCGGCGCTTGTTCCAAAAGCTGAAATTGAAGGTGACATGGGTGATTCACACGTCGGTTTACAGGCGCGTCTCATGTCTCAGGCGCTCCGTAAGCTTTCCGGCGCCATCAATAAATCTAAAACAATCGCAATCTTTATTAACCAGATTCGTGAAAAAGTCGGCGTTATGTTCGGAAATCCGGAGACGACACCGGGCGGCCGCGCGCTGAAA-TTCTATTCTTCCGTGCGTCT--TGAAGTGCGCCGTGCCGAG-CAATTAAAGCAGGGCAACGACGTTATGGGGAATAAA-ACGAGAATTAAAGTCGTAAAAAAC Bacillus_velezensis_CR502_T_NZ_LHCC1000001 AAGGTTCCATCATGAAGCTCGGAGAAAAAACGGATACAAGAATTTCAACGGTGCCAAGCGGTTCCCTTGCACTTGATACCGCTCTCGGAATAGGCGGATACCCGCGCGGACGGATTATTGAAGTATACGGACCTGAAAGCTCAGGTAAAACGACTGTAGCGCTTCACGCAATCGCTGAGGTTCAGGAAAAAGGCGGACAGGCAGCATTTATTGATGCTGAGCATGCTCTTGATCCTGTTTACGCGCAAAAGCTCGGTGTCAATATCGAAGAGCTTCTGCTTTCTCAGCCGGATACGGGAGAGC---AGGCGCTAGAGATTGCAGAAGCGCTGGTGCGAAGCGGAGCGGTTG-ATATCGTAGTCGTTGACTCTGTTGCGGCGCTTGTTCCAAAAGCTGAAATTGACGGTGACATGGGTGATTCGCACGTCGGTTTACAAGCTCGTCTCATGTCTCAGGCGCTCCGTAAGCTTTCCGGCGCCATCAATAAATCTAAAACAATCGCAATCTTTATTAACCAGATTCGTGAAAAAGTCGGCGTTATGTTCGGAAATCCGGAGACGACACCGGGCGGCCGCGCGCTGAAA-TTCTATTCTTCCGTGCGCCT--TGAAGTGCGCCGTGCCGAG-CAATTAAAGCAGGGCAACGACGTCATGGGGAATAAA-ACGAGAATTAAAGTCGTAAAAAAC Bacillus_vallismortis_DSM_11031_T_NZ_JH600197 AAGGTTCCATCATGAAGCTCGGAGAAAAAACGGATACAAGAATTTCAACGGTGCCAAGCGGTTCCCTTGCACTTGATACCGCTCTCGGAATAGGCGGATACCCGCGCGGACGGATTATTGAAGTATACGGACCTGAAAGCTCAGGTAAAACGACTGTAGCGCTTCACGCAATCGCTGAGGTTCAGGAAAAAGGCGGACAGGCAGCATTTATTGATGCTGAGCATGCTCTTGATCCTGTTTACGCGCAAAAGCTCGGTGTCAATATCGAAGAGCTTCTGCTTTCTCAGCCGGATACGGGAGAGC---AGGCGCTAGAGATTGCAGAAGCGCTGGTGCGAAGCGGAGCGGTTG-ATATCGTAGTCGTTGACTCTGTTGCGGCGCTTGTTCCAAAAGCTGAAATTGACGGTGACATGGGTGATTCGCACGTCGGTTTACAAGCTCGTCTCATGTCTCAGGCGCTCCGTAAGCTTTCCGGCGCCATCAATAAATCTAAAACAATCGCAATCTTTATTAACCAGATTCGTGAAAAAGTCGGCGTTATGTTCGGAAATCCGGAGACGACACCGGGCGGCCGCGCGCTGAAA-TTCTATTCTTCCGTGCGCCT--TGAAGTGCGCCGTGCCGAG-CAATTAAAGCAGGGCAACGACGTCATGGGGAATAAA-ACGAGAATTAAAGTCGTAAAAAAC Bacillus_coagulans_NBRC_12583_T_CP009709 AGGGCTCCATTATGCGGCTGGGCGAGCAGACCGACCGGGTTGTCTCCACGATCCCGACCGGTTCGCTTGCGCTTGATATTGCCCTTGGTGTCGGCGGCTACCCGCGCGGCCGCGTCATTGAAATATATGGCCCTGAAAGTTCCGGTAAAACAACGGTTGCCCTGCATGCGATTGCGGAAGTCCAGGCACAGGGCGGACAGGCTGCCTTTATTGATGCGGAACACGCACTTGACCCGGTTTATGCCCAAAAGCTCGGTGTCAACATTGATGAACTGCTCCTGTCCCAGCCGGATACGGGCGAAC---AGGCGCTGGAAATTGCAGAAGCGCTCGTCCGCAGCGGCGCAGTGG-ACATTGTTGTCATTGACTCCGTTGCTGCGCTTGTGCCGAGAGCGGAAATTGAAGGGGAAATGGGCGATTCCCATGTCGGCCTCCAGGCACGGCTGATGTCCCAGGCGCTGCGGAAATTATCGGGTGCGATCAACAAATCAAACACGATTGCGATTTTCATTAACCAAATCCGGGAAAAAGTCGGCGTGATGTTCGGCAATCCTGAAGTCACACCGGGCGGACGCGCGCTCAAG-TTTTACTCGTCCGTACGCCT--TGAAGTGCGCCGTGCCGAA-CAGATCAAACAAGGGAGCGACATTGTCGGCAACAAA-ACGAAAATCAAGGTTGTCAAAAAC Bacillus_licheniformis_DSM_13_T_AE017333 AAGGTTCGATTATGAAACTCGGCGAACAAACTGAAACGAGAATTTCAACAGTTCCGAGCGGTTCTTTAGCGCTCGATGCGGCTCTTGGAGTGGGCGGATACCCGCGCGGCCGGATTATTGAAGTATACGGGCCTGAAAGCTCCGGTAAAACGACGGTGGCGCTTCATGCGATTGCCGAAGTTCAGCAGCAGGGCGGACAAGCGGCGTTCATCGACGCCGAACACGCGCTTGATCCCGTCTATGCACAAAAGCTGGGCGTCAACATTGATGAGCTTTTGCTGTCACAGCCTGATACGGGCGAGC---AGGCGCTCGAAATCGCTGAAGCCCTTGTCAGAAGCGGAGCGGTGG-ATATCGTTGTCATCGACTCTGTAGCAGCGCTTGTGCCGAAAGCTGAAATCGAAGGAGATATGGGGGATTCCCACGTCGGTTTGCAGGCCAGACTGATGTCTCAGGCGCTTCGCAAGCTTTCCGGAGCGATCAATAAATCGAAGACCATCGCGATCTTTATCAACCAGATTCGTGAAAAAGTCGGTGTCATGTTTGGAAATCCTGAGACGACGCCAGGCGGAAGAGCGCTGAAA-TTCTACTCTTCTGTCCGCCT--TGAAGTGCGCCGCGCAGAG-CAGCTGAAACAAGGCAACGACGTCATGGGGAACAAG-ACGAAAATCAAAGTCGTGAAAAAC Bacillus_methylotrophicus_CBMB_205_T_NZ_CP011937 CGGATTTGTTCCTGAATCATCAGCATGATGTCTTTATTTTCTTTTAAGAACTGCTTGGCGTTTTCACGGCCCTGACCGAGGCGTTCTTCTTCATAAGAATACCACG-AACCGCTTTTTTGCACGATATCCAGTTCAGTTCCAAGGTCGA-TGATTTCCCCTTCTTTGGAGATTCCTTCACCGTACATAATGTCCACTTCAGCCGTACGGAACGGAG-GAGCGACTTTGTTTTTTACGACTTTAATTCTCGTTTTATTCCCCATGACGTCGTTGCCCTGCTTTAATTGCTCGGCACGGCGCACTTCAAGGCGCACGGAAGAATAGAATTTC-AGCGCGCGGCCGCCCGGTGTCGTCTCCGGATTTCCGAACATAACGCCGACTTTTTCACGAATCTGGTTAATAAAGATTGCAATTGTTTTAGATTTATTGATGGCGCCGGAAAGCTTACGGAGCGCCTGAGACATGAGACGCGCCTGTAAACCGACGTGTGAATCACCCATGTCACCTTCAATTTCAGCTTTTGGAACAAGCGCCGCAACAGAGTCAACGACTACGATATCA-ACAGCTCCGCTTCGCACCAGCGCTTCAGCAATCTCAAGCGCCTGCTCTCCCGTATCCGGCTGAGAAAGCAGAAGCTCTTCGATATTGACACCGAGCTTTTGCGCGTAAACAGGATCAAGAGCATGC Bacillus_subtilis_LMG_7135_T_CP015375 CGAATTTGCTCCTGGATCATCAGCATGATATCTTTATTTTCTTTCAGGAATTGTTTTGCATTTTCACGGCCTTGGCCAAGACGCTCTTCTTCATAAGAGTACCATG-AACCGCTTTTTTGCACGATATCAAGTTCAGTTCCTAGATCAA-TGATTTCGCCTTCTTTTGAAATGCCTTCTCCGTACATAATGTCAACCTCGGCTGTACGGAACGGCG-GAGCCACCTTGTTTTTCACGACTTTGATTTTCGTTTTGTTCCCCATTACGTCGTTGCCTTGTTTCAGCTGTTCAGCACGGCGCACTTCAAGACGCACGGAAGAATAGAATTTC-AACGCACGGCCGCCAGGTGTTGTTTCCGGGTTCCCGAACATAACACCGACTTTTTCACGAATTTGGTTAATGAAAATCGCGATTGTCTTCGATTTGTTAATGGCCCCTGAAAGCTTACGAAGCGCTTGAGACATTAAGCGTGCTTGTAAACCGACATGCGAATCTCCCATGTCGCCTTCAATTTCCGCTTTCGGAACGAGAGCGGCTACAGAGTCGACAACGACAATGTCA-ACTGCCCCGCTTCGAACCAATGCTTCCGCAATTTCAAGCGCCTGCTCGCCTGTGTCAGGCTGAGACAGTAAAAGCTCTTCGATGTTAACACCGAGCTTTTGCGCGTATACCGGATCTAACGCATGC ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 689; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 689; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 689; END; BEGIN TREES; Title recA_Bacillus_spp._NJ_analysis; ID 016b3ec5d0713; LINK Taxa = Bacillus_spp.; TRANSLATE [0] 1 A6_MH750312, [1] 2 Bacillus_amyloliquefaciens_DSM7_T_FN597644, [2] 3 Bacillus_velezensis_CR502_T_NZ_LHCC1000001, [3] 4 Bacillus_vallismortis_DSM_11031_T_NZ_JH600197, [4] 5 Bacillus_coagulans_NBRC_12583_T_CP009709, [5] 6 Bacillus_licheniformis_DSM_13_T_AE017333, [6] 7 Bacillus_methylotrophicus_CBMB_205_T_NZ_CP011937, [7] 8 Bacillus_subtilis_LMG_7135_T_CP015375; TREE Imported_tree_1 = ((((1:0.0,4:0.0):0.0[%bootstrapFrequency = 0.328 ],3:0.0):0.01141507[%bootstrapFrequency = 1 ],2:0.00977383):0.01257772[%bootstrapFrequency = 0.631 ],(5:0.19482666,6:0.09309484):0.09700074[%bootstrapFrequency = 0.743 ],(7:0.0942232,8:0.08278018):1.39789652[%bootstrapFrequency = 1 ])[% ] [% ] [% setBetweenDouble = bootstrapFrequency ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1560227933717; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3315986979515565446; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 1382684399341963549; mqVersion 360; checksumv 0 3 201211817 null getNumChars 689 numChars 689 getNumTaxa 8 numTaxa 8 short true bits 15 states 15 sumSquaresStatesOnly 112347.0 sumSquares 112347.0 longCompressibleToShort false usingShortMatrix true 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 1366 649; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3315986979515565446 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3315986979515565446; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3315986979515565446 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016b3ec5d0713; toggleUseWeights off; endTell; setAssignedID 1042.1560126286373.7122779213183056826; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; 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; setSelectedTaxonHighlightMode 1; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; setTaxonNameStyler #mesquite.trees.NoColorForTaxon.NoColorForTaxon; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName off; 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; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; toggleShow consensusFrequency; toggleShow posteriorProbability; toggleShow bootstrapFrequency; setDigits 4; setThreshold ?; writeAsPercentage off; toggleCentred off; toggleHorizontal on; toggleWhiteEdges on; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #1382684399341963549 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1266 577; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; 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; togglePaleMissing off; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; 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 16 6 1 1; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;