#NEXUS [written Tue Jun 18 11:48:33 EDT 2019 by Mesquite version 3.6 (build 917) at JE1_win7/10.38.193.38] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=15; TAXLABELS Tomato_ringspot_virus_KR911671.1_CHILE Tomato_ringspot_virus_KR911670.1_CHILE Tomato_ringspot_virus_KM083894.1_CANADA Tomato_ringspot_virus_CAES_Wild14 Tomato_ringspot_virus_HM776008.1_MD_USA Tomato_ringspot_virus_MF176959.1_OH_USA Tomato_ringspot_virus_KR911672.1_CHILE Tomato_ringspot_virus_CAES_New44 Tomato_ringspot_virus_HM776005.1_MD_USA Tomato_ringspot_virus_KR911669.1_CHILE Tomato_ringspot_virus_L19655.1 Tomato_ringspot_virus_D12477.2_CANADA Tomato_ringspot_virus_KM083891.1_CANADA Tomato_ringspot_virus_HM775998.1_MD_USA Tomato_ringspot_virus_U46022.1_NY_USA ; END; BEGIN CHARACTERS; TITLE ToRSV; DIMENSIONS NCHAR=321; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Tomato_ringspot_virus_KR911671.1_CHILE CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGTCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_KR911670.1_CHILE CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGTCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_KM083894.1_CANADA CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTTT-----CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_CAES_Wild14 CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGAAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_HM776008.1_MD_USA CCCGGCCTTTCTT-CCGGTACAATACCTAGCGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAATGAAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTTTTTTTCCTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACGCGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_MF176959.1_OH_USA CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGAAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTGCGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGCTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_KR911672.1_CHILE CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGTCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_CAES_New44 CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGAAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_HM776005.1_MD_USA CCCGGCCTTTCTT-CCGGTATAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_KR911669.1_CHILE CCCGGCCTTTCTT-CCGGTACAATACCTAGTGAAGCAAGCAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTGCTTAACGGAGGAATATGTCGTGTTTTCTACACGTTAGTGTTGCATTGCTATAATGGCAATGTAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGG-CCTAAGATGGCCAGCACACGGTACGATTAAATTTAGTTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_L19655.1 CCCGGCCTTCCTT-CCGGTACAATACCTAGTGAAGCAAGTAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTACTTAAGGAAGGAATATGTCGTGTTTTCCACACGTTAGTGTTGCAATGCTGTAATGGCACTGCAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGCTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_D12477.2_CANADA CCCGGCCTTCCTT-CCGGTACAATACCTAGTGAAGCAAGTAATTGCGTTGAGGGATAAGAGTAGCATGTTCCTACTTAAGGAAGGAATATGTCGTGTTTTCCACACGTTAGTGTTGCAATGCTGTAATGGCACTGCAGTGCAGGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGTCACAATTGTGTGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGTCTGGAAGTGATTACCAGGGCCTAAGATGGCCAGCACACGGTACGATTAAATTTAGCTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_KM083891.1_CANADA CCGGTTCTTTCTTACCGGTACAATACCTGGCGAAGCGAATA-TTGCGTCGAGGGATGAGAGTAGCATGTTCCTGCTCATTGAAGGAATATGTCGTGTTTTCTGCACGTTAGTGTTATG-ACGCTATCCAGCGCCATAGTGCAAGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGACACAATTGCATGTGTACTGTTGACGGAGGAGTAGCGATCCTCTATCACGCAGGGCCGGAAGTAATTCCCGGGGCCGAAGAAGGCCAGCATGCGGTACGATTAACTTTAGCTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_HM775998.1_MD_USA CCGGTTCTTTCTTACCGGTACAATACCTGGCGAAACGAATA-TTGCGTCGAGGGATGAGAGTAGCATGTTCCTGCTCATTGAAGGAATATGTCGTGTTTTCTACACGTTAGTGTTATG-ACGCTACCCAGCGCCATAGTGCAAGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGACACAATTGTATGTGTACTGTTGACGGAGGAGTAGCGATCCTCTACCACGCAGGGCCGGAAGTGATTCCCGGGGCCGAAGAAGGCCAGCATGCGGTACGATTAACTTTAGCTGTAATGTAGTGGTATGTTA Tomato_ringspot_virus_U46022.1_NY_USA CCGGTTCTTTCTTACCGGTACAATACCTGGTGAAGCGAATACTTGCGTCGAGGGATGAGAGTAGCATGTTCCTACTCATTGAAGGAATATGTCGTGTTTTCCACACGTTAGTGTTAAATGCAGTACCCAGCGCCATAGTGCAAGAATGGTTCCCAGCCACTTTTT------CTGGGATTCTAATCGTACGACACAATTGCATGTGTATCGTTGACGGAGGAGTAGCGATCCTCTACCACGCGAGCCTGGAAGTAATTGCCGGGGCCGAAGAAGGCCAGCATGCGGTACGATTAACTTTAGCTGTAATGTAGTGGTATGTTA ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 321; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 321; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 321; END; BEGIN TREES; Title ToRSV; ID 016b6b3c4ade12; LINK Taxa = Taxa; TRANSLATE [0] 1 Tomato_ringspot_virus_KR911671.1_CHILE, [1] 2 Tomato_ringspot_virus_KR911670.1_CHILE, [2] 3 Tomato_ringspot_virus_KM083894.1_CANADA, [3] 4 Tomato_ringspot_virus_CAES_Wild14, [4] 5 Tomato_ringspot_virus_HM776008.1_MD_USA, [5] 6 Tomato_ringspot_virus_MF176959.1_OH_USA, [6] 7 Tomato_ringspot_virus_KR911672.1_CHILE, [7] 8 Tomato_ringspot_virus_CAES_New44, [8] 9 Tomato_ringspot_virus_HM776005.1_MD_USA, [9] 10 Tomato_ringspot_virus_KR911669.1_CHILE, [10] 11 Tomato_ringspot_virus_L19655.1, [11] 12 Tomato_ringspot_virus_D12477.2_CANADA, [12] 13 Tomato_ringspot_virus_KM083891.1_CANADA, [13] 14 Tomato_ringspot_virus_HM775998.1_MD_USA, [14] 15 Tomato_ringspot_virus_U46022.1_NY_USA; TREE Imported_tree_1 = (((((((2,7)[%bootstrapFrequency = 0.236 ],1)[%bootstrapFrequency = 0.65 ],(9,(3,10)[%bootstrapFrequency = 0.196 ])[%bootstrapFrequency = 0.142 ])[%bootstrapFrequency = 0.642 ],(4,8)[%bootstrapFrequency = 0.321 ])[%bootstrapFrequency = 0.669 ],5)[%bootstrapFrequency = 0.528 ],6)[%bootstrapFrequency = 0.822 ],(11,12)[%bootstrapFrequency = 0.999 ],(15,(13,14)[%bootstrapFrequency = 0.939 ])[%bootstrapFrequency = 1 ])[% ] [% ] [% setBetweenBits = selected setBetweenDouble = bootstrapFrequency ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1560872914152; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7879342667130276288; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3737356408204980166; mqVersion 360; checksumv 0 3 824325046 null getNumChars 321 numChars 321 getNumTaxa 15 numTaxa 15 short true bits 15 states 15 sumSquaresStatesOnly 113795.0 sumSquares 113795.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 161; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 906; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7879342667130276288 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016b6b3c4ade12; toggleUseWeights off; endTell; setAssignedID 4400.1560872248621.7779285806655896819; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1119 834; 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; newAssistant #mesquite.trees.TreeLegendMaker.TreeLegendMaker; tell It; setOffsetsX 4; setOffsetsY 4; getLegendsVector; tell It; distributeCommands; setBounds 4 4 115 23; setOffsetX 4; setOffsetY 4; endDistributeCommands; endTell; calculate; endTell; 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 bootstrapFrequency; toggleShow posteriorProbability; 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 #3737356408204980166 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 244; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1119 834; setLocation -8 -8; 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; 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;