#NEXUS [written Tue Jun 11 01:33:58 ART 2019 by Mesquite version 3.6 (build 917) at Nazareno-PC/192.168.56.1] BEGIN TAXA; TITLE Pseudomonas_spp.; DIMENSIONS NTAX=11; TAXLABELS Pseudomonas_azotoformans_IAM_1603_T_AB039411 Pseudomonas_putida_NBRC_14164_T_AP013070 Pseudomonas_migulae_CCUG_43165_T_FN554204 Pseudomonas_gessardii_CIP_105469_T_FN554186 Pseudomonas_brenneri_DSM_15294_T_JN589902 Pseudomonas_yamanorum_8H1_T_EU557346 Pseudomonas_proteolytica_CIP_108464_T_FN554220 Pseudomonas_panacis_CIP_108524_T_FN554214 Pseudomonas_granadensis_F_278770_T_HG764749 BT1L_MH750314 MPe3L_MH760410 ; END; BEGIN CHARACTERS; TITLE gyrB_Pseudomonas_spp.; DIMENSIONS NCHAR=516; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pseudomonas_azotoformans_IAM_1603_T_AB039411 GCCAAGCGTATTCGTGAACTGTCGTTCCTTAACTCCGGCGTGGGTATCGTCCTCAAGGACGAGCGCAGCGGCAAGGAAGAGCTGTTCAAGTACGAAGGCGGCTTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCTCAGCGCGACGGCGGTACTCACTTGGTGGGTTTCCGTTCCGCACTGACGCGTAACCTGAACACCTACATCGAAGCCGAAGGTTTGGCCAAGAAGCATAAAGTCGCCACTACCGGTGACGATGCGCGCGAAGGCCTGACTGCGATTATCTCGGTGAAAGTGCCGGATCCGAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCTTCCGAAGTGAAGACCGCAGTGGAACAGGAGATGGGCAAATACTTCTCC Pseudomonas_putida_NBRC_14164_T_AP013070 GCCAAGCGTATTCGCGAGTTGTCGTTCCTCAACTCGGGCGTTGGCATTCTGCTGAAGGATGAGCGCAGCGGTAAGGAAGAGTTCTTCAAATACGAAGGCGGCCTGCGTGCGTTCGTCGAGTACCTGAACACCAACAAGACGCCAGTCAACTCCCAGGTGTTCCACTTCAGCGTTCAGCGTGAAGACGGCGTGGGCGTGGAAGTTGCTTTGCAGTGGAACGACAGCTTCAACGAAAACCTGCTGTGCTTCACCAACAACATTCCACAGCGCGACGGTGGCACCCACTTGGTGGGCTTCCGTTCTTCGCTGACCCGTAGCCTGAACAGCTACATCGAACAGGAAGGCCTGGCGAAGAAGAACAAGGTGGCGACCACGGGTGACGACGCCCGTGAAGGCCTGACCGCGATCATCTCGGTGAAGGTACCGGACCCCAAGTTCAGCTCGCAGACCAAAGACAAGCTGGTTTCCTCGGAGGTGAAAACCGCCGTGGAACAGGAGATGAACAAGTACTTCTCT Pseudomonas_migulae_CCUG_43165_T_FN554204 GCCAAGCGGATTCGTGAACTGTCCTTCCTGAACTCCGGTGTCGGCATCGTCCTCAAGGATGAGCGCAGCGGCAAGGAAGAGTTGTTCAAGTACGAAGGTGGCTTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACTCCAGTCAAT---CAGGTGTTCCACTTCAACATTCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAATGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATCCCGCAGCGCGATGGGGGGACTCACCTGGTGGGTTTCCGCTCCGCTCTGACGCGTAACCTGAACACTTACATCGAAGCTGAAGGCCTGGCCAAGAAGCACAAGGTTGCCACCACCGGTGATGACGCCCGTGAAGGCTTGACCGCGATCATCTCGGTGAAGGTGCCGGATCCTAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCTTCCGAAGTGAAGACCGCGGTCGAACAGGAAATGGGCAAGTACTTCTCC Pseudomonas_gessardii_CIP_105469_T_FN554186 GCCAAGCGGATTCGTGAGCTGTCCTTCCTCAACTCCGGTGTGGGTATCGTCCTCAAGGACGAGCGCAGCGGCAAGGAAGAGCTGTTCAAATACGAAGGTGGCCTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAATATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCCCAGCGCGACGGCGGTACTCACCTGGTGGGTTTCCGTTCCGCACTGACGCGTAACCTGAACACCTACATCGAAGCCGAAGGCCTGGCGAAGAAGCACAAAGTCGCCACCACCGGTGACGATGCCCGCGAAGGCCTGACTGCGATTATTTCGGTCAAGGTGCCAGACCCAAAGTTCAGCTCCCAGACCAAGGACAAGCTGGTTTCTTCTGAAGTGAAGACCGCTGTCGAACAGGAAATGGGCAAGTACTTCTCC Pseudomonas_brenneri_DSM_15294_T_JN589902 GCCAAGCGGATTCGTGAACTGTCCTTCCTCAACTCCGGTGTGGGTATCGTCCTCAAGGACGAGCGCAGCGGCAAGGAAGAACTGTTCAAGTACGAAGGCGGCCTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCTCAGCGCGATGGCGGTACTCACCTGGTGGGTTTCCGTTCCGCCCTGACGCGTAACCTGAACACCTACATCGAAGCTGAAGGCCTGGCGAAGAAGCACAAAGTCGCCACCACCGGTGATGATGCGCGTGAAGGCCTGACCGCAATTATTTCGGTCAAGGTTCCGGATCCGAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTTTCTTCCGAAGTGAAGACCGCTGTCGAACAGGAAATGGGTAAGTACTTCTCT Pseudomonas_yamanorum_8H1_T_EU557346 GCCAAGCGGATTCGTGAATTGTCCTTCCTCAACTCCGGTGTGGGTATCGTCCTCAAGGACGAGCGCAGCGGCAAGGAAGAGCTGTTCAAATACGAAGGTGGCCTGCGTGCGTTCGTTGAATACTTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCTCAGCGCGATGGCGGTACTCACCTGGTGGGTTTCCGTTCGGCACTGACGCGTAACCTGAACACCTACATCGAAGCAGAAGGCCTGGCGAAGAAGCACAAAGTCGCCACCACCGGTGACGATGCCCGTGAAGGCCTGACCGCGATTATTTCGGTCAAGGTTCCGGATCCGAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCTTCCGAAGTGAAGACCGCCGTTGAACAGGAAATGGGCAAGTACTTCTCC Pseudomonas_proteolytica_CIP_108464_T_FN554220 GCCAAGCGGATTCGTGAACTGTCGTTCCTCAACTCCGGTGTGGGTATCGTCCTCAAGGACGAACGCAGCGGCAAGGAAGAGCTGTTCAAGTACGAAGGTGGTCTGCGTGCATTCGTTGAATACCTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAATGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCCCAGCGCGACGGCGGTACTCACTTGGTGGGTTTCCGTTCTGCACTGACGCGCAACCTGAACACCTACATCGAAGCCGAAGGCCTGGCCAAGAAGCACAAGGTCGCCACCACCGGTGACGATGCCCGTGAAGGCCTGACTGCGATTATTTCGGTCAAGGTCCCGGATCCCAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTTTCTTCTGAAGTGAAGACCGCTGTTGAACAGGAAATGGGCAAGTATTTCTCC Pseudomonas_panacis_CIP_108524_T_FN554214 GCCAAGCGGATTCGTGAATTGTCCTTCCTCAACTCCGGTGTCGGCATCGTCCTCAAGGATGAGCGCAGCGGCAAGGAAGAGCTATTCAAATACGAAGGTGGCTTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACTGCGGTCAAC---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTGGAAATCGCCCTGCAATGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCACAGCGTGACGGTGGTACTCACCTGGTGGGTTTCCGTTCGGCGCTGACGCGTAACCTGAACACCTATATCGAAGCCGAAGGCCTGGCGAAGAAGCATAAGGTCGCCACCACCGGTGACGATGCCCGTGAAGGCCTGACCGCAATCATCTCGGTGAAAGTGCCGGACCCTAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCTTCCGAAGTGAAAACTGCGGTTGAACAGGAGATGGGTAAGTACTTCTCC Pseudomonas_granadensis_F_278770_T_HG764749 GCCAAGCGGATTCGTGAACTGTCCTTCCTCAACTCCGGTGTCGGCATCGTCCTCAAGGATGAGCGCAGCGGCAAGGAAGAGCTTTTCAAATACGAAGGCGGCCTGCGCGCGTTCGTTGAATACCTGAACACCAACAAGACCGCGGTCAAT---CAGGTGTTCCACTTCAATATCCAGCGCGAAGACGGCATCGGCGTGGAAGTTGCGCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCGCAACGCGATGGCGGTACTCACCTGGTGGGCTTCCGTTCGGCGCTGACGCGTAACCTGAACAACTACATCGAACAGGAAGGCCTGGCGAAGAAACACAAAGTCGCCACCACTGGCGATGATGCCCGTGAGGGCCTGACTGCGATCATCTCGGTGAAAGTACCGGATCCGAAGTTCAGCTCGCAGACCAAAGACAAGCTGGTGTCTTCCGAAGTGAAGACCGCCGTCGAGCAGGAGATGGGCAAGTACTTCTCC BT1L_MH750314 GCCAAGCGGATTCGTGAACTGTCTTTCCTGAACTCCGGTGTGGGTATCGTCCTCAAGGACGAACGCAGCGGCAAGGAAGAGCTGTTCAAGTACGAAGGCGGCCTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACCGCGGTCAAT---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTAGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCTCAGCGCGATGGCGGTACTCACCTGGTGGGTTTCCGTTCTGCACTGACGCGTAACCTGAACACCTACATCGAAGCGGAAGGCCTGGCGAAGAAACACAAAGTCGCCACCACCGGTGACGATGCCCGCGAAGGCCTGACCGCCATTATCTCGGTCAAGGTTCCGGATCCGAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCCTCCGAAGTGAAGACAGCGGTCGAACAGGAAATGGGCAAGTACTTCTCC MPe3L_MH760410 GCCAAGCGGATTCGTGAACTGTCTTTCCTGAACTCCGGTGTGGGTATCGTCCTCAAGGACGAACGCAGCGGCAAGGAAGAGCTGTTCAAGTACGAAGGCGGCCTGCGTGCGTTCGTTGAATACCTGAACACCAACAAGACCGCGGTCAAT---CAGGTGTTCCACTTCAACATCCAGCGTGAAGACGGCATCGGCGTAGAAATCGCCCTGCAGTGGAACGACAGCTTCAACGAGAACCTGTTGTGCTTCACCAACAACATTCCTCAGCGCGATGGCGGTACTCACCTGGTGGGTTTCCGTTCTGCACTGACGCGTAACCTGAACACCTACATCGAAGCGGAAGGCCTGGCGAAGAAACACAAAGTCGCCACCACCGGTGACGATGCCCGCGAAGGCCTGACCGCCATTATCTCGGTCAAGGTTCCGGATCCGAAGTTCAGCTCCCAGACCAAAGACAAGCTGGTGTCCTCCGAAGTGAAGACAGCGGTCGAACAGGAAATGGGCAAGTACTTCTCC ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 516; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 516; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 516; END; BEGIN TREES; Title gyrB_Pseudomonas_spp._NJ_analysis; ID 016b375bb90122; LINK Taxa = Pseudomonas_spp.; TRANSLATE [0] 1 Pseudomonas_azotoformans_IAM_1603_T_AB039411, [1] 2 Pseudomonas_putida_NBRC_14164_T_AP013070, [2] 3 Pseudomonas_migulae_CCUG_43165_T_FN554204, [3] 4 Pseudomonas_gessardii_CIP_105469_T_FN554186, [4] 5 Pseudomonas_brenneri_DSM_15294_T_JN589902, [5] 6 Pseudomonas_yamanorum_8H1_T_EU557346, [6] 7 Pseudomonas_proteolytica_CIP_108464_T_FN554220, [7] 8 Pseudomonas_panacis_CIP_108524_T_FN554214, [8] 9 Pseudomonas_granadensis_F_278770_T_HG764749, [9] 10 BT1L_MH750314, [10] 11 MPe3L_MH760410; TREE Imported_tree_1 = ((((((((10:0.0,11:0.0):0.02677526[%bootstrapFrequency = 1 ],5:0.01900888):0.00061345[%bootstrapFrequency = 0.286 ],6:0.01365899):0.00341543[%bootstrapFrequency = 0.394 ],(4:0.01878683,7:0.02517357):0.00704544[%bootstrapFrequency = 0.771 ]):0.00207955[%bootstrapFrequency = 0.397 ],1:0.03745913):0.01369242[%bootstrapFrequency = 0.879 ],3:0.0428439):0.00164472[%bootstrapFrequency = 0.387 ],8:0.03340881):0.0142031[%bootstrapFrequency = 0.742 ],9:0.0417595,2:0.12826077)[% ] [% ] [% setBetweenDouble = bootstrapFrequency ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1560227638592; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9014090857327317868; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 7967004183645403422; mqVersion 360; checksumv 0 3 1540904876 null getNumChars 516 numChars 516 getNumTaxa 11 numTaxa 11 short true bits 15 states 15 sumSquaresStatesOnly 102546.0 sumSquares 102546.0 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 700 472; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #9014090857327317868 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #9014090857327317868; getWindow; tell It; useTargetValue off; setTargetValue ; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 400; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 #9014090857327317868 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016b375bb90122; toggleUseWeights off; endTell; setAssignedID 2978.1560001894827.1700356068088380935; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 400; setLocation 8 8; 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; 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 #7967004183645403422 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 400; setLocation 8 8; 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;