#NEXUS [written Tue Jun 18 14:00:01 EDT 2019 by Mesquite version 3.6 (build 917) at JE1_win7/10.38.193.38] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=21; TAXLABELS Grapevine_leafroll_associated_virus_1_AF195822.1_AUSTRALIA Grapevine_leafroll_associated_virus_1_CAES_RU3 Grapevine_leafroll_associated_virus_1_CAES_Ru6 Grapevine_leafroll_associated_virus_1_CAES_Sun1 Grapevine_leafroll_associated_virus_1_CAES_Sun2 Grapevine_leafroll_associated_virus_1_CAES_Sun4 Grapevine_leafroll_associated_virus_1_EF103901.1_CANADA Grapevine_leafroll_associated_virus_1_AY644650.1_CZECH_REPUBLIC Grapevine_leafroll_associated_virus_1_MG925332.1_FRANCE Grapevine_leafroll_associated_virus_1_KP866939.1_SLOVENIA Grapevine_leafroll_associated_virus_1_MF446625.1_HUNGARY Grapevine_leafroll_associated_virus_1_KP866943.1_SLOVENIA Grapevine_leafroll_associated_virus_1_KP866945.1_SLOVENIA Grapevine_leafroll_associated_virus_1_KU674796.1_WA_USA Grapevine_leafroll_associated_virus_1_KU674797.1_WA_USA Grapevine_leafroll_associated_virus_1_MH807214.1_CANADA Grapevine_leafroll_associated_virus_1_MH807215.1_CANADA Grapevine_leafroll_associated_virus_1_MH807216.1_CANADA Grapevine_leafroll_associated_virus_1_KM034909.2_TURKEY Grapevine_leafroll_associated_virus_1_MK317844.1_VA_USA Grapevine_leafroll_associated_virus_1_MK317842.1_WA_USA ; END; BEGIN CHARACTERS; TITLE GLRaV1; DIMENSIONS NCHAR=150; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Grapevine_leafroll_associated_virus_1_AF195822.1_AUSTRALIA ATTTTTCCTAAAGGTCACCCAGTACCATCAGTATATGAAACGAGCTTTCAAGTATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGTACTTGGATGAATGAGATCGCTTTTAAGGGTACGGACTACAGACCATCT Grapevine_leafroll_associated_virus_1_CAES_RU3 ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAGCAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_CAES_Ru6 ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAGCAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_CAES_Sun1 ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAACAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_CAES_Sun2 ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAACAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_CAES_Sun4 ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAACAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_EF103901.1_CANADA ATATTTCCCAAAGGTCACCCGATACCGTCGGTATACGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGAATTTTTGAAGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACAGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_AY644650.1_CZECH_REPUBLIC ATTTTTCCCAAAGGTCACCCGGTACCGTCGGTATATGAAACGAGCTTTCAAGTATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGTACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MG925332.1_FRANCE ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAACTTTCAAATATCAGGAAGTACTATGGAGTACGGTATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KP866939.1_SLOVENIA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MF446625.1_HUNGARY ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGACCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTCGAGGGTGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KP866943.1_SLOVENIA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGTACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KP866945.1_SLOVENIA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAACATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KU674796.1_WA_USA ATTTTTCCAAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAATACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KU674797.1_WA_USA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTATGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MH807214.1_CANADA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATAGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MH807215.1_CANADA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCTCTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MH807216.1_CANADA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_KM034909.2_TURKEY ATTTTTCCCAAAGGTCATCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCAGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAATGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MK317844.1_VA_USA ATTTTTCCCAAAGGTCACCCGATACCGTCGGTATATGAAACGAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAACCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT Grapevine_leafroll_associated_virus_1_MK317842.1_WA_USA ATTTTTCCCAAAGGTCACCCGATACCGTCAGTATATGAAACAAGCTTTCAAATATCGGGAAGCACTATGGAGTACGGCATTTTTGAGGGCGAGTCTAATCGCACCTGGTTGAACGAGATCGCTTTTAAGGGGACGGACTACAGACCGTCT ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 150; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 150; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 150; END; BEGIN TREES; Title GLRaV1; ID 016b6bbcaeaf26; LINK Taxa = Taxa; TRANSLATE [0] 1 Grapevine_leafroll_associated_virus_1_AF195822.1_AUSTRALIA, [1] 2 Grapevine_leafroll_associated_virus_1_CAES_RU3, [2] 3 Grapevine_leafroll_associated_virus_1_CAES_Ru6, [3] 4 Grapevine_leafroll_associated_virus_1_CAES_Sun1, [4] 5 Grapevine_leafroll_associated_virus_1_CAES_Sun2, [5] 6 Grapevine_leafroll_associated_virus_1_CAES_Sun4, [6] 7 Grapevine_leafroll_associated_virus_1_EF103901.1_CANADA, [7] 8 Grapevine_leafroll_associated_virus_1_AY644650.1_CZECH_REPUBLIC, [8] 9 Grapevine_leafroll_associated_virus_1_MG925332.1_FRANCE, [9] 10 Grapevine_leafroll_associated_virus_1_KP866939.1_SLOVENIA, [10] 11 Grapevine_leafroll_associated_virus_1_MF446625.1_HUNGARY, [11] 12 Grapevine_leafroll_associated_virus_1_KP866943.1_SLOVENIA, [12] 13 Grapevine_leafroll_associated_virus_1_KP866945.1_SLOVENIA, [13] 14 Grapevine_leafroll_associated_virus_1_KU674796.1_WA_USA, [14] 15 Grapevine_leafroll_associated_virus_1_KU674797.1_WA_USA, [15] 16 Grapevine_leafroll_associated_virus_1_MH807214.1_CANADA, [16] 17 Grapevine_leafroll_associated_virus_1_MH807215.1_CANADA, [17] 18 Grapevine_leafroll_associated_virus_1_MH807216.1_CANADA, [18] 19 Grapevine_leafroll_associated_virus_1_KM034909.2_TURKEY, [19] 20 Grapevine_leafroll_associated_virus_1_MK317844.1_VA_USA, [20] 21 Grapevine_leafroll_associated_virus_1_MK317842.1_WA_USA; TREE Imported_tree_1 = (((((((((17,20)[%bootstrapFrequency = 0.081 ],15)[%bootstrapFrequency = 0.018 ],13)[%bootstrapFrequency = 0.008 ],10)[%bootstrapFrequency = 0.005 ],(16,18)[%bootstrapFrequency = 0.053 ])[%bootstrapFrequency = 0.072 ],(7,(11,(19,(9,12)[%bootstrapFrequency = 0.397 ])[%bootstrapFrequency = 0.219 ])[%bootstrapFrequency = 0.141 ])[%bootstrapFrequency = 0.141 ])[%bootstrapFrequency = 0.274 ],14)[%bootstrapFrequency = 0.429 ],((2,3)[%bootstrapFrequency = 0.691 ],(4,(5,(6,21)[%bootstrapFrequency = 0.134 ])[%bootstrapFrequency = 0.05 ])[%bootstrapFrequency = 0.13 ])[%bootstrapFrequency = 0.866 ])[%bootstrapFrequency = 0.781 ],8,1)[% ] [% ] [% setBetweenDouble = bootstrapFrequency ]; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1560880801511; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 1784474829898015838; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5563309497228114779; mqVersion 360; checksumv 0 3 4206317796 null getNumChars 150 numChars 150 getNumTaxa 21 numTaxa 21 short true bits 15 states 15 sumSquaresStatesOnly 67980.0 sumSquares 67980.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 906; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #1784474829898015838 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 016b6bbcaeaf26; toggleUseWeights off; endTell; setAssignedID 5700.1560880714054.7605016644533132671; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 834; setLocation -8 0; 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 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 #5563309497228114779 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 115; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1180 834; 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;