#NEXUS [written Thu Jun 23 21:37:12 CDT 2011 by Mesquite version 2.74 (build 550) at Home-PC/192.168.2.2] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS 1_1689_51 9_1586_22 11_1588_1 10_1695_1 5_1696_1_8_mix 6_1697_2 7_1692_T_J_mix 3_1505_1 4_1589_51 2_1590_1 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=139; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 1_1689_51 GGTTTTGATGCATTAGTTGCATTTTTGTATGTAAGTAGAAGACTTATGTCTAGCTTGTAAGTGTATTACAGATTTCTGTATTTTGGAGTCTTTTTGCTCGTAATAAGAATTTTGGTTGGGTAACAAAATTACATAAGTT 9_1586_22 GGGTTTGATCTATTCAGTACTTCGTTTGACATAATTGATAGATCTTATACGAGATTGTGGATATGTTTTTATATTTCTTTTGAGTTGGTTGAATGTCTATTTGTTGTTAGTTGTATATGAAGTAATGTCCAGGATTTCG 11_1588_1 AGGTTTGATCTATTCAGTATTTCATTTGACATGATTGATAGACCTTATACGGGATTGTGGATATGTTTTTATATTTCCTTTAGATTGGTTGAATATTCACTTATTGTTAGTTATATTTGAAGTAATGTCCAGGATTTTG 10_1695_1 GGGTTTGGTCTATTCAGTATTTCATTTGACATAATTGATAGACCTTATACGGGATTGTGGATATGTTTTTATATTTCCTTTAAATTGGTTGAGTATCCACCTATTGTTAGTTATATATGAAGTAATGTCCAGGATTTTG 5_1696_1_8_mix GAATCTGGTTTATTTAGTGTTTCATCTGACATAGTTGATAGACTCTATACGCGGTTGTGAATATGTTTTTATTTTTCCTTTAAACTGGTTGTATATTCGTCTGTTGTTAGTTATGTATGAAGTAATGTCCAGGGCTTCG 6_1697_2 GGGTTTGGTCTATTCAGTATTTCATTTGACATAATTGATAGACCTTATACGAGATTGTGGATATGTTTTTATATTTCTTTTAAGTTTGTTGAATATCCATTTATTGTTAGTTGTATATGAAGTAATGTCCAGGATTTCG 7_1692_T_J_mix AGATCTAATTTATTCAGTGTTTCATTTGACATAGTAAATAGACTTTATACGCGATTGTGGATATGTTTTTGTTTTCCCTTTAGACTGGTTGTATATTTGTCTATTGTTAGTTGTGTATGAAGTAATATCCAGGGCTTCG 3_1505_1 AAGTTTGATTTCTTCGGTGCTTCATCTGATATAGTTGAAATTTCCTGGCCTAGATTAAAGGTATGTTTTTATCTTTTCTCTAGGCTGGTTGTATATCTGGTTTTTAGTAATTGGGCGTGGAGGAGTGTCCGAAGGCTCG 4_1589_51 GAGTTTGGTTTCTTCGGTACGTCATCTGATATAGTCGAAAATTCCTGGCTTGGATTGAAGGTATGTTTTTATCTTTTCTCTAGGCTGATTGTATATCTGGTCTTTAGTAATTGGGCGTGGAGAAGTGTCTGAAGGTTCG 2_1590_1 TGGTCTAATACGAACAGTGTATTGCTATACATAAATGAGAAACTCAAGTTGGTATTGTAGGTGTATTTTTTATTTTTCTGTGTAATGGTAGTACATCTGTTAAACTGTAGTTTTATGTGTAGTAGATAATGGAAATTCG ; END; BEGIN TREES; Title 'Trees from "louse4fold.txt"'; LINK Taxa = Taxa; TRANSLATE 1 1_1689_51, 2 9_1586_22, 3 11_1588_1, 4 10_1695_1, 5 5_1696_1_8_mix, 6 6_1697_2, 7 7_1692_T_J_mix, 8 3_1505_1, 9 4_1589_51, 10 2_1590_1; TREE PAUP_1 = (1,(((((2,6),(3,4)),(5,7)),(8,9)),10)); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 139; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 139; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 139; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1308883033001; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3735755815903910305; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 2407968632390046657; mqVersion 274; checksumv 0 2 1035900619 null getNumChars 139 numChars 139 getNumTaxa 10 numTaxa 10 short true bits 15 states 15 sumSquaresStatesOnly 44584.0 sumSquares 44584.0 NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3735755815903910305 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1708.1308883006987.8616000649830122493; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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; 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 #2407968632390046657 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;