#NEXUS [written Thu Aug 02 16:00:21 EDT 2012 by Mesquite version 2.74 (build 550) at Jeremy-Andersen.local/192.168.1.103] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=17; TAXLABELS Binodoxys_acalephae_JN620600 Binodoxys_sp_FJ798202 Binodoxys_communis_FJ798201 Binodoxys_communis_HQ599570 Hymenoptera_sp_JN288968 Hymenoptera_sp_HQ929630 Hymenoptera_sp_HQ929671 Trioxys_pallidus_JN620696 Trioxys_pallidus_JN620695 Trioxys_pallidus_J0097 Trioxys_pallidus_J0100 Trioxys_pallidus_J0101 Trioxys_pallidus_J0102 Trioxys_pallidus_J0090 Trioxys_pallidus_J0093 Trioxys_pallidus_J0094 Hymenoptera_sp_JN292906 ; END; BEGIN CHARACTERS; TITLE 'Trioxys: Alignment of COI from museum specimens of Trioxys pallidus and closely related species from Genbank'; DIMENSIONS NCHAR=684; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Binodoxys_acalephae_JN620600 -ATTTTATATTTTATATTTGGTATATGATCTGGTATGGTTGGTTTATCAATAAGATTAATTATTCGTATAGAATTAAGAATTCCTGGTAGGTTAATTGGTAATGATCAGATTTATAATAGTATTGTTACCGCTCATGCTTTTGTTATAATTTTTTTTATGGTTATACCAATTATAATTGGTGGATTTGGTAATTGGTTGATTCCTTTGATATTAGGGGCTCCTGATATAGCTTTTCCTCGTATGAATAATATAAGATTTTGATTACTAATTCCTTCTTTAATTTTATTATTAGTTAGGGGACTAATAAATGTAGGGGTAGGTACTGGTTGAACTGTTTATCCTCCATTATCATTGAATTTAGGTCATAGTGGTATTTCTGTTGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCATCAATTATAGGTGCAATTAATTTTATTAGAACTATTTTAAATATACGTTCCTATAGAGTATCTATAGATCAGATTTCATTATTAGTTTGATCAGTATTAATTACAGCTATTTTATTATTATTATCATTACCTGTATTGGCGGGTGCAATTACTATATTATTATTTGATCGTAATTTAAATACTAC------------------------------------------------------------------------------ Binodoxys_sp_FJ798202 TATTTTATATTTTATATTTGGTATATGATCTGGTATAGTTGGTCTATCAATAAGATTAATTATTCGTATAGAATTAAGAATTCCTGGTAGATTAATTGGTAATGATCAGATTTATAATAGTATTGTTACAGCTCATGCTTTTGTAATAATTTTTTTTATGGTTATACCAATTATAATTGGTGGGTTTGGTAATTGATTGATTCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCTCGGATGAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTATTATTAGTTAGGGGATTAATAAATGTAGGTGTTGGTACTGGGTGAACTGTGTATCCTCCATTATCATTGAATTTAGGTCATAGTGGTATTTCTGTTGATTTAGCTATTTTTTCTTTGCATTTAGCAGGTATTTCATCAATTATAGGCGCAATTAATTTTATTAGAACTATTTTAAATATACGTTCTTATAGAGTATCTATAGATCAGATTTCATTATTAGTTTGATCAGTATTAATTACAGCTATTTTATTATTATTATCATTACCTGTATTGGCGGGTGCAATTACTATATTATTATTTGATCGTAATTTAAATACTACTTTTTTTGATTTTGGTGGTGGTGGGGATCCAATTTTATATCAGCATTTATTTTGATTTTTTGGTCACCCTGAAGTTTA Binodoxys_communis_FJ798201 TATTTTATATTTTATATTTGGTATATGATCTGGTATAGTTGGTCTATCAATAAGATTAATTATTCGTATAGAATTAAGAATTCCTGGTAGATTAATTGGTAATGATCAGATTTATAATAGTATTGTTACAGCTCATGCTTTTGTAATAATTTTTTTTATGGTTATACCAATTATAATTGGTGGGTTTGGTAATTGGTTGATTCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCTCGGATGAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTATTATTAGTTAGGGGATTAATAAATGTAGGTGTTGGTACTGGGTGAACTGTGTATCCTCCATTATCATTGAATTTAGGTCATAGTGGTATTTCTGTTGATTTAGCTATTTTTTCTTTGCATTTAGCAGGTATTTCATCAATTATAGGCGCAATTAATTTTATTAGAACTATTTTAAATATACGTTCTTATAGAGTATCTATAGATCAGATTTCATTATTAGTTTGATCAGTATTAATTACAGCTATTTTATTATTATTATCATTACCTGTATTGGCGGGTGCAATTACTATATTATTATTTGATCGTAATTTAAATACTACTTTTTTTGATTTTGGTGGTGGTGGGGATCCAATTTTATATCAGCATTTATTTTGATTTTTTGGTCACCCTGAAGTTTA Binodoxys_communis_HQ599570 TATTTTATATTTTATATTTGGTATATGATCTGGTATAGTTGGTCTATCAATAAGATTAATTATTCGTATAGAATTAAGAATTCCTGGTAGATTAATTGGTAATGATCAGATTTATAATAGTATTGTTACAGCTCATGCTTTTGTAATAATTTTTTTTATGGTTATACCAATTATAATTGGTGGGTTTGGTAATTGGTTGATTCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCTCGGATGAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTATTATTAGTTAGGGGATTAATAAATGTAGGTGTTGGTACTGGGTGAACTGTGTATCCTCCATTATCATTGAATTTAGGTCATAGTGGTATTTCTGTTGATTTAGCTATTTTTTCTTTGCATTTAGCAGGTATTTCATCAATTATAGGCGCAATTAATTTTATTAGAACTATTTTAAATATACGTTCTTATAGAGTATCTATAGATCAGATTTCATTATTAGTTTGATCAGTATTAATTACAGCTATTTTATTATTATTATCATTACCTGTATTGGCGGGTGCAATTACTATATTATTATTTGATCGTAATTTAAATACTACTTTTTTTGATTTTGGTGGTGGTGGGGATCCAATTTTATATCAGCATTTAT---------------------------- Hymenoptera_sp_JN288968 TATTTTATATTTTATATTTGGTATATGGTCAGGTATGGTTGGTTTATCTATAAGTTTAATTATTCGTATAGAGTTAAGTATTCCAGGAAGATTAATTGGTAATGATCAAATTTATAATAGAATTGTTACTGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGGGGTTTTGGAAATTGATTAATTCCTTTAATATTAGGGGCTCCGGATATGGCTTTCCCACGAATAAATAATATAAGATTTTGATTATTAATTCCTTCATTAATTTTATTAGTAATTAGAGGTTTAATAAATGTGGGTGTGGGTACTGGTTGAACAGTTTATCCTCCATTATCTTTAAATTTGGGTCATAGTGGTATTTCTGTTGATTTGGCAATTTTTTCTTTACATTTAGCTGGTATTTCTTCAATTATAGGGGCTATTAATTTTATTAGAACAATTTTAAATATACGATCTTATGGGGTTTCAATAGATCAGATTCCTTTATTGATTTGATCAGTTCTTATTACAGCTATTTTGTTATTATTGTCTTTACCTGTTTTAGCGGGTGCTATTACTATATTATTATGTGATCGTAATTTAAATACTACTTTTTTTGATTTTGCAGGAGGGGGGGATCCAATTTTATATCAGCATTTATTT-------------------------- Hymenoptera_sp_HQ929630 TATTTTATATTTTATGTTTGGTATATGGGCGGGGATGGTTGGTCTTTCAATAAGTTTAATTATCCGTATAGAGTTAAGTATTCCTGGTAGTTTAATTGGTAATGATCAGATTTATAATAGTATTGTTACTGCTCATGCTTTTGTTATAATTTTTTTTATGGTCATGCCCATTATAATTGGGGGGTTTGGTAATTGATTAATTCCTCTTATATTGGGGGCTCCTGATATAGCTTTCCCTCGTATGAATAATATGAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTAGGGGTTTAATAAATGTAGGGGCTGGTACGGGTTGAACTGTTTATCCTCCTTTATCTTTAAATTTGGGCCATAGTGGTATTTCGGTTGATTTAGCTATTTTTTCTCTACATTTAGCTGGTATTTCTTCAATTATAGGGGCAATTAATTTTATTAGAACAATTTTAAATATGCGTTCTTACGGGGTTTCTATGGATCAGGTTTCTTTGTTGATTTGATCTGTTTTAATTACAGCTATTTTGTTATTGTTATCATTGCCGGTATTGGCTGGGGCTATTACCATATTGTTATGTGACCGTAATTTAAATACTACGTTTTTTGATTTTGCTGGTGGGGGTGACCCTGTTCTTTACCAACATTTATTT-------------------------- Hymenoptera_sp_HQ929671 TATTTTATATTTTATATTTGGTATATGGTCTGGGATAGTTGGTTTATCAATAAGGTTAATTATTCGTATAGAGTTGAGAATTCCTGGGAGGTTAATTGGCAATGATCAGATTTATAATAGGATTGTTACAGCACATGCTTTTGTTATAATTTTTTTTATAGTTATACCAATTATAATTGGTGGATTTGGTAATTGGTTAATTCCTTTGATATTAGGGGCTCCTGATATAGCTTTTCCTCGTATAAATAATATAAGTTTTTGATTATTAATTCCTTCATTGATTTTGTTATTAGTTAGAGGTTTAATAAATGTGGGGGTAGGTACTGGGTGGACTGTTTATCCTCCATTATCTTTAAATTTAGGTCATAGTGGTATTGCAGTAGATTTAGCTATTTTTTCTTTGCATTTAGCCGGTATTTCATCTATTATGGGTGCAATTAATTTTATTAGTACTATTTTAAATATACGTTCATATAATGTTTCAATGGATCAGATTTCGTTATTAGTTTGGTCAGTATTAATTACAGCTATTTTGTTGTTATTATCATTACCTGTGTTAGCGGGAGCTATTACAATATTATTATTCGATCGTAATTTAAATACTACTTTTTTTGATTTTGGAGGAGGAGGGGATCCGATTTTGTATCAACATTTATTT-------------------------- Trioxys_pallidus_JN620696 TATTTTATATTTTATGTTTGGTATATGGGCGGGTATGGTTGGTCTATCAATAAGTTTAATTATTCGTATAGAGTTAAGTATTCCTGGTAGTTTAATTGGCAATGATCAGATTTATAATAGTATTGTTACTGCTCATGCTTTTGTTATAATTTTTTTTATAGTTATGCCTATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTAGGGGTTTAATAAATGTAGGGGCTGGTACAGGTTGAACTGTTTACCCGCCTTTATCTTTAAATTTGGGCCATAGGGGTATTTCGGTTGATTTGGCTATTTTTTCTTTACATTTAGCTGGTATTTCTTCAATTATGGGTGCAATTAATTTTATTAGTACAATTTTAAATATACGTTCTTATGGGGTTTCTATGGATCAGGTTTCCTTGTTGATTTGGTCTGTTTTAATTACTGCTATTTTGTTGTTATTATCTTTGCCTGTATTGGCGGGGGCTATTACAATATTGTTATGTGATCGTAATTTAAATACTACGTTTTTTGATTTTGCTGGGGGAGGGGACCCA----------------------------------------------- Trioxys_pallidus_JN620695 TATTTTATATTTTATGTTTGGTATATGGGCGGGTATGGTTGGTCTATCAATAAGTTTAATTATTCGTATAGAGTTAAGTATTCCTGGTAGTTTAATTGGCAATGATCAGATTTATAATAGTATTGTTACTGCTCATGCTTTTGTTATAATTTTTTTTATAGTTATGCCTATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTAGGGGTTTAATAAATGTAGGGGCTGGTACAGGTTGAACTGTTTACCCGCCTTTATCTTTAAATTTGGGCCATAGGGGTATTTCGGTTGATTTGGCTATTTTTTCTTTACATTTAGCTGGTATTTCTTCAATTATGGGTGCAATTAATTTTATTAGTACAATTTTAAATATACGTTCTTATGGGGTTTCTATGGATCAGGTTTCCTTGTTGATTTGGTCTGTTTTAATTACTGCTATTTTGTTGTTATTATCTTTGCCTGTATTGGCGGGGGCTATTACAATATTGTTATGTGATCGTAATTTAAATACTACGTTTTTTGATTTTGCTGGGGGAGGGGACCCA----------------------------------------------- Trioxys_pallidus_J0097 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0100 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTCCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0101 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTCCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0102 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGTTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCTCCTGATATAGCTTTCCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0090 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGGTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCCCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0093 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGCTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCCCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trioxys_pallidus_J0094 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATAATTGGGGGCTTTGGTAATTGATTGATTCCTTTAATATTGGGGGCCCCTGATATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTAATTCCTTCTTTAATTTTGTTATTAATTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Hymenoptera_sp_JN292906 TATTTTGTATTTTATATTTGGCATATGATCTGGCATGGTTGGTTTATCTATAAGATTAATTATTCGTATAGAGTTAAGAATTCCTGGTAGATTAATTGGTAATGATCAAATTTATAATAGTATTGTTACAGCTCATGCTTTTGTTATAATTTTTTTTATGGTTATACCAATTATAATTGGTGGATTTGGTAATTGATTAATTCCTTTAATATTAGGGGCCCCCGATATGGCTTTTCCTCGAATAAATAATATAAGATTTTGATTATTAATCCCTTCTTTAATTTTATTATTAGTTAGAGGATTAATAAATGTAGGGGTAGGGACTGGTTGAACTGTTTATCCCCCATTGTCATTAAATTTAGGTCATAGAGGTATTTCAGTTGATTTGGCTATTTTTTCTTTACATTTAGCTGGTATTTCATCAATTATAGGTGCAATTAATTTTATTAGAACAATTTTAAATATACGGTCTTATAGAGTATCTATGGATCAGATTTCATTACTAGTTTGATCAGTATTAATTACAGCTATTTTATTATTATTATCATTACCTGTATTAGCGGGGGCAATTACTATATTATTATTTGATCGTAATTTAAATACAACTTTTTTTGATTTTGGTGGTGGCGGGGATCCTATTTTATAC-------------------------------------- ; END; BEGIN TREES; Title 'Trioxys: Set of 2 MP Trees from analysis of COI data for Trioxys'; LINK Taxa = Taxa; TRANSLATE 1 Binodoxys_acalephae_JN620600, 2 Binodoxys_sp_FJ798202, 3 Binodoxys_communis_FJ798201, 4 Binodoxys_communis_HQ599570, 5 Hymenoptera_sp_JN288968, 6 Hymenoptera_sp_HQ929630, 7 Hymenoptera_sp_HQ929671, 8 Trioxys_pallidus_JN620696, 9 Trioxys_pallidus_JN620695, 10 Trioxys_pallidus_J0097, 11 Trioxys_pallidus_J0100, 12 Trioxys_pallidus_J0101, 13 Trioxys_pallidus_J0102, 14 Trioxys_pallidus_J0090, 15 Trioxys_pallidus_J0093, 16 Trioxys_pallidus_J0094, 17 Hymenoptera_sp_JN292906; TREE Trioxys_MP_Tree_1 = (1:2.0,(2:1.0,3:0.0,4:0.0):3.0,(((5:5.0,(6:6.0,((8:0.0,9:0.0,10:0.0,(14:1.0,15:0.0,16:0.0):2.0):1.0,11:0.0,12:0.0,13:0.0):1.0):4.0):5.0,17:3.0):3.0,7:5.0):2.0); TREE Trioxys_MP_Tree_2 = (1:2.0,(2:1.0,3:0.0,4:0.0):3.0,(((5:5.0,(6:6.0,((8:0.0,9:0.0,10:0.0,(14:1.0,(15:0.0,16:0.0):0.0):2.0):1.0,11:0.0,12:0.0,13:0.0):1.0):4.0):5.0,17:3.0):3.0,7:5.0):2.0); END; BEGIN CODONS; CODONPOSSET * UNTITLED = N: 1- 684 ; CODONPOSSET CodonPositions = N: 1- 684 ; CODESET * UNTITLED = universal: 1 - 684; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 684; EXSET * UNTITLED = 1 - 168 297 - 684; END; BEGIN MacClade; Version 4.0 87; LastModified -884103390; FileSettings editor '0' '0' '1' '1'; Singles 100; Editor 00011001111111100100010010 '1' '12' Geneva '9' '100' '1' all; EditorPosition '44' '6' '819' '1371'; TreeWindowPosition '46' '6' '831' '1390'; ListWindow Characters closed Geneva '9' '50' '10' '129' '399' 000; ListWindow Taxa closed Geneva '9' '50' '10' '129' '490' 100000000; ListWindow Trees closed Geneva '9' '50' '10' '276' '490'; ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ListWindow ExSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharSets closed Geneva '9' '50' '10' '276' '490'; ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490'; ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490'; ListWindow WtSets closed Geneva '9' '50' '10' '276' '490'; ChartWindowPosition '52' '30' '818' '1380'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder; OtherSymbols & / 00 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '705' '46' '115' '165'; TreeWindowProgram 10; TreeWindow 0000; Continuous '0' '3' 1; Calculations 0000001; SummaryMode '0' '0' 0; Charts Geneva '9' ( normal ) 0010; NexusOptions '0' '0' '48' 001000101; TipLabel '1'; TreeFont Geneva '9' ( normal ); TreeShape 1.0 1.0 0100; TraceLabels 0101; ChartColors '0' '0' '65535' '9' '0' 1; ChartBiggestSpot 1; ChartPercent 10; ChartBarWidth '10' 1; ChartVerticalAxis 10101; ChartMinMax '0'; TraceAllChangesDisplay '1' 1; BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101; ContinuousBranchLabels 0; AllStatesBranchLabels 1; IndexNotation '2' 1; PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '0' '0' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000; MatchChar 00 .; EntryInterpretation 01; ColorOptions 00; TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110; EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '1' 100010101110011; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010; BothTools '1'; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 684; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1343937622026; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 482756935379184824; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3209629464500676824; mqVersion 274; checksumv 0 2 3420700608 null getNumChars 684 numChars 684 getNumTaxa 17 numTaxa 17 short true bits 15 states 15 sumSquaresStatesOnly 242844.0 sumSquares 242844.0 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 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #482756935379184824 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1067.1328123801821.7526518260770634155; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 22; 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 #3209629464500676824 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 278; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; 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;