#NEXUS [written Fri Jul 18 16:19:51 EDT 2014 by Mesquite version 2.75 (build 566) at Taylors-MacBook-Pro.local/192.168.1.3] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=9; TAXLABELS 'Grapevine fleck virus GU372367-Chardonnay-USA' 'Grapevine fleck virus GU372370-Chardonnay-USA' 'Grapevine fleck virus GU372369-Chardonnay-USA' 'Grapevine fleck virus GU372371-Chardonnay-USA' 'Grapevine fleck virus AJ309022-Unknown-Italy' 'Grapevine fleck virus GU372368-Chardonnay-USA' 'Grapevine fleck virus KF417610-Chancellor-USA *' 'Grapevine fleck virus KF417611-Albarino-USA *' 'Grapevine red globe virus AF521977-GRGV Outgroup' ; END; BEGIN CHARACTERS; TITLE Grapevine_fleck_virus_Replicase_sequences; DIMENSIONS NCHAR=464; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Grapevine fleck virus GU372367-Chardonnay-USA' AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCTCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTTATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ATGCCCTCA 'Grapevine fleck virus GU372370-Chardonnay-USA' AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCTCTTACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCTTG-CATG-ATGCCCTCA 'Grapevine fleck virus GU372369-Chardonnay-USA' AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ACGCCCTCA 'Grapevine fleck virus GU372371-Chardonnay-USA' AACACCATCCAGAAGGACA-CGATCGCCTCCTCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGC----TGGCC-CTCCGCCCTCAACCAAGCCGGCATCCCCGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCCATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGTCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ATGCCCTCA 'Grapevine fleck virus AJ309022-Unknown-Italy' AACACAATCCAGAAGGATA-CGATCGCCTCCTCCATC--ATTGCCGCCCTCAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCCCGCGC----TGGCC-CTCCGCCCTCAACCAAGCCGGCATCCCCGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATT--GAAACCCATCTCCTCCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGC------GTCTCCAACGCGGCTCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATC-ATTCCCTCA 'Grapevine fleck virus GU372368-Chardonnay-USA' AACACCATCCAGAAGGACA-CGATCGCCTCGTCCATC--ATCGCGGCCCTCAACCCATCCCTCACCTCATCCCTCACTCTCTATCCCTACG-CGCTCCCCGCGCGT----TGGCC-CGCAGCCCTCAACCACGCCGGCATCCCCGCCA----CCTCCTATGGCCACCAATCCCACCCCCACCCCATCCATAA-GACCATC--GAAACCCACCTCCTTCACGAACACTGGGCTAACCGTGCCACCCTCCCCTCCACGGTCATG-TTCATGAAGCGATCCAAGTT---TGACAAGCTCCGC------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATTCTTACCGCTCGCGACG---CCGATCGGTACACCCAC-ATGCCCCTTCCCGAATCCCTTCCCTCCACTCCCCTCTACTTCATG-CATG-ACGCCCTCA 'Grapevine fleck virus KF417610-Chancellor-USA *' AACACCATCCAGAAGGACA-CGATCGCCTCCTCCATC--ATAGCCGCTCTCAACCCCTCCCTCACCTCCTCTCTCACCCTCTATCCCTACG-CCCTCCCGGCGCGT----TGGCC-GTCCGCGCTCAACCACGCCGGAATCCCTGCCA----CCTCCTACGGCCACCAATCCCATCCTCACCCCATCCATAA-GACCATT--GAAACCCATCTCCTCCATGAGCACTGGGCTAACCGCGCCACCCTCCCTTCCACCGTCCTG-TTCATGAAGAGGTCGAAGTT---TGACAAGCTCCGG------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGTGACG---CCGACCGTTACACCCAC-ATGCCCCTCCCCGACACCCTCCCGTCAACCCCCCTCTACTTCATG-CATG-ACGCCCTCG 'Grapevine fleck virus KF417611-Albarino-USA *' AAGAGTGTCTGGAAGGACA-CGATCGCGTCTTCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGC----TGGCC-TTCCGCCCTCAACCAAGCCGGCATCCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCCATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGCGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTTCCCCTCCCCGACACCCTCCCTTCCACCCCTCTCTATTTCATG-CATG-ATGCCCTCA 'Grapevine red globe virus AF521977-GRGV Outgroup' TCCATCCCTCAGCCCCTCATCGATCTCCACGTGCATCTGAAGACCAACGTGGACACCCAACTCGGCCCCCTCACCTCCATGCGCCTCACTGGCGAACCAGGAACGTATGATGACAACTCTGATTACAACCTGGCCGTCACTGCAGCCAAATTCATCCTA-GACCCCGAGGTCCACGCCGTTCTCATCTCCGGCGACGATCTTGACATCTCCCCCCCCCCTCCAGTCCGCCCCACCTGGCCCATTCTCGAAGCCATGCTCTCACTTCGCTTCAAGACTGAAGTCTCCCGCTACGGTCTTTTCTGCGGTTACTATCTTGGCCCCGCTGGAGCCGTCCGCTCACCTCTGGCCCTCTTTGCCAAGCTCATCATCGCCGTCGACGACGGTTCCATCGAGGACAAGAAAGCTTCATATCTCTCAGAATTTGCTGTCGGCCACTCCCTCGGTCAGGACATGTGGACTCTC- ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 464; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 464; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 464; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1405714791874; linkFile GFkV_tree_GenBank_IDs_from_MEGA.nwk.nex; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4192600318445582766; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2922991294838270214; mqVersion 275; checksumv 0 3 2103964224 null getNumChars 464 numChars 464 getNumTaxa 9 numTaxa 9 short true bits 15 states 15 sumSquaresStatesOnly 65906.0 sumSquares 65906.0 longCompressibleToShort false usingShortMatrix true NumFiles 2 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1182 585; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4192600318445582766 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4192600318445582766; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 8 22; 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 #4192600318445582766 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlockInt 0; toggleUseWeights off; endTell; setAssignedID 1890.1405709023561.3044658743697861210; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; 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 on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree 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; setDigits 4; writeAsPercentage off; toggleCentred on; 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 #2922991294838270214 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 8 22; 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; 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 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.chromaseq.ColorQuality.ColorQuality; tell It; toggleAmbiguities on; toggleMarks on; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; getEmployee #mesquite.chromaseq.SourceFileInfoEditor.SourceFileInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;