#NEXUS [written Thu Aug 02 15:21:45 EDT 2012 by Mesquite version 2.74 (build 550) at Jeremy-Andersen.local/192.168.1.103] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=13; TAXLABELS Doryctes_sp_GU173830 Atanycolus_simplex_GU173831 Digonogastra_sp_GU173829 Atanycolus_longifemoralis_J0086 Atanycolus_longifemoralis_J0087 Atanycolus_longifemoralis_J0088 Atanycolus_longifemoralis_J0089 Atanycolus_ulmicola_GU173828 Atanycolus_ulmicola_GU173832 Atanycolus_ulmicola_GU173833 Atanycolus_sp_GU173826 Atanycolus_sp_GU173827 Atanycolus_hicoriae_GU173825 ; END; BEGIN CHARACTERS; TITLE Alignment_of_COI_from_museum_specimens_of_Atanycolus_longifemoralis_and_congeners_from_GenBank; DIMENSIONS NCHAR=615; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Doryctes_sp_GU173830 GGTATTATATTTTTTATTTGGAATTTGGTCAGGTATAATTGGGTTATCAATAAGAATAATTATTCGTTTAGAATTAGGTATACCAGGGAGTTTATTAGGAAATGATCAAATTTATAATATAATAGTGACTTTACATGCTTTCATTATAATTTTTTTTATAGTTATACCTGTTATGTTGGGTGGATTTGGAAATTGATTAGTACCTTTAATGTTAGGGGCTCCTGATATATCTTTTCCACGTATAAATAATATAAGATTTTGATTATTGGTGCCTTCAGTAATTTTATTATTATTTAGAGGATTTGTTAATGTGGGGGCAGGAACGGGGTGAACAATATATCCTCCTTTATCTTCAAGAATAGGTCATCCTGGGGTATCTGTAGATATGGCTATTTTTTCATTACATTTAGCAGGGGTATCATCTATTATAGGATCTATTAATTTTATTACTACTGTATTTAATATATCTTTATATATGATTAAAATGGATCAAATTATATTATTAGTTTGATCAGTTTTAATTACTACTTTTTTATTATTATTATCACTTCCGGTTTTAGCTGGGGCTATTACTATATTATTAACGGATCGTAATTTGAGAACTACATTTTTTGA Atanycolus_simplex_GU173831 AATATTATATTTTTTTTTTGGAATATGATCAGGAATATTAGGTTTATCTATAAGACTCATTATCCGATTGGAGTTAGGAACTCCAGGAAGAATATTAGGTAATGATCAATTATATAATAGAATAGTTACATCCCATGCTTTTATTATAATTTTTTTTATAGTAATACCAATTATATTAGGAGGATTTGGAAATTGATTAATTCCTTTAATATTAGGTGCTCCAGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTTATCCCTTCATTAATTTTATTAATTTTAAGAAGTTTTACAAGTAATGGTGTTGGAACAGGATGAACTGCTTACCCTCCTTTATCATCCACTTTAGGACATAGAAGAATTTCGGTAGATTTAGCAATTTTTTCTTTACATATAGCTGGAATTTCATCAATTATAGGATCAATTAATTTTATTACAACAATTTTAAATATACGTCTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTATTTGATCAATTTTTATTACAACAATTTTATTATTATTATCTTTACCTGTCTTAGCAGGAGGAATTACTATATTATTAACAGATCGAAATTTAAATACTACTTTTTTTGA Digonogastra_sp_GU173829 AATTTTATATTTTTTATTTGGTATATGAGCTGGTATATTAGGGTTATCTATAAGATTAATTATTCGATTAGAATTAGGTATACCAGGAAGTTTATTAGGTAACGATCAAATTTATAATAGTATAGTTACAGCACATGCATTTATTATAATTTTTTTTATGGTTATACCAATTATATTAGGAGGATTTGGAAATTGATTACTTCCTTTAATATTAGGAGCTCCTGATATAGCTTTCCCTCGTATAAATAATATGAGATTTTGGTTAATTATTCCTTCTTTAATTTTATTATTAATAAGAAGAATTTTAAATGTAGGAGTAGGGACAGGTTGAACAGTTTATCCTCCTTTATCATCTTCCTTAGGTCATAGTGGTTTATCTGTTGATTTAGCAATTTTTTCATTACATATTGCTGGTATTTCGTCTATTATAGGATCAATTAATTTTATTTCTACAATTTTAAATATACATTTAATTTTATTAAAATTAGATCAATTAACTTTATTTATTTGATCAATTTTTATTACAACTATTTTATTATTATTATCTTTACCAGTTTTAGCAGGAGCTATTACAATATTATTAACAGATCGAAATTTAAATACATCATTTTTTGA Atanycolus_longifemoralis_J0086 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTATAGTAGGAGGATTTGGTAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTCCCTCGAATAAATAATATGAGGTTTTGATTATTAGTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Atanycolus_longifemoralis_J0087 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTATAGTAGGAGGATTTGGTAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTCCCTCGAATAAATAATATGAGGTTTTGATTATTAGTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Atanycolus_longifemoralis_J0088 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTATAGTAGGAGGATTTGGTAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTCCCTCGAATAAATAATATGAGGTTTTGATTATTAGTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Atanycolus_longifemoralis_J0089 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTATAGTAGGAGGATTTGGTAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTCCCTCGAATAAATAATATGAGGTTTTGATTATTAGTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Atanycolus_ulmicola_GU173828 AATATTGTATTTTTTTTTTGGAATATGGGCTGGTATAGTAGGTTTATCAATAAGATTAATTATTCGTTTAGAATTGGGTTTACCTGGTAGAATATTGGGTAATGATCAAATTTATAATAGAATAGTAACTTCACATGCTTTTGTTATAATTTTTTTTATAGTAATACCAATTATATTAGGGGGTTTTGGAAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTTCCTCGAATAAATAATATAAGATTTTGATTATTATTTCCTTCATTAATATTATTAATTTTAAGTGGATTTGTTAATGTTGGGGTTGGAACTGGATGAACAGTTTATCCTCCTTTATCTTCTATTATAGGTCATTCAGGTATTTCTGTTGATTTAGTTATTTTTTCTTTACATATAGCTGGTATTTCATCAATTATAGGTTCAATTAATTTTATTACAACTATTTTAAATATACGTTTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTGTTTGATCAATTTTTATTACAACAATTTTATTATTATTATCATTACCTGTATTAGCTGGGGGTATTACAATATTATTAACTGATCGAAATTTAAATACAACATTTTTTGA Atanycolus_ulmicola_GU173832 AATATTGTATTTTTTTTTTGGAATATGGGCTGGTATAGTAGGTTTATCAATAAGATTAATTATTCGTTTAGAATTGGGTTTACCTGGTAGAATATTGGGTAATGATCAAATTTATAATAGAATAGTAACTTCACATGCTTTTGTTATAATTTTTTTTATAGTAATACCAATTATATTAGGGGGTTTTGGAAATTGATTAATTCCTTTAATATTAGGGGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGATTATTATTTCCTTCATTAATTTTATTAATTTTAAGTGGATTTGTTAATGTTGGGGTTGGAACTGGATGAACAGTTTATCCTCCTTTATCTTCTATTATAGGTCATTCAGGTATTTCTGTTGATTTAGTTATTTTTTCTTTACATATAGCTGGTATTTCATCAATTATAGGTTCAATTAATTTTATTACAACTATTTTAAATATACGTTTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTGTTTGATCAATTTTTATTACAACAATTTTATTATTATTATCATTACCTGTATTAGCTGGGGGTATTACAATATTATTAACTGATCGAAATTTAAATACAACATTTTTTGA Atanycolus_ulmicola_GU173833 AATATTGTATTTTTTTTTTGGAATATGGGCTGGTATAGTAGGTTTATCAATAAGATTAATTATTCGTTTAGAATTGGGTTTACCTGGTAGAATATTGGGTAATGATCAAATTTATAATAGAATAGTAACTTCACATGCTTTTGTTATAATTTTTTTTATAGTAATACCAATTATATTAGGGGGTTTTGGAAATTGATTAATTCCTTTAATATTAGGGGCTCCAGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGATTATTATTTCCTTCATTAATTTTATTAATTTTAAGTGGATTTGTTAATGTTGGGGTTGGAACTGGATGAACAGTTTATCCTCCTTTATCTTCTATTATAGGTCATTCAGGTATTTCTGTTGATTTAGTTATTTTTTCTTTACATATAGCTGGTATTTCATCAATTATAGGTTCAATTAATTTTATTACAACTATTTTAAATATACGTTTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTGTTTGATCAATTTTTATTACAACAATTTTATTATTATTATCATTACCTGTATTAGCTGGGGGTATTACAATATTATTAACTGATCGAAATTTAAATACAACATTTTTTGA Atanycolus_sp_GU173826 TATATTATATTTTTTATTTGGTATGTGGTCGGGAATTTTAGGTTTATCTATAAGATTAATTATTCGATTAGAATTGGGGATACCTGGGAGTTTATTAGGAAATGACCAAATTTATAATGGTTTAGTTACATCACATGCTTTTGTTATAATTTTTTTTATGGTTATACCAATTATGGTAGGTGGATTTGGAAATTGATTAATTCCTTTAATATTAGGGGTTCCTGACATAGCTTTCCCACGTATAAATAATATGAGTTTTTGATTATTAATTCCTTCATTAATTTTATTAATTTTAAGAGGATTTGTAAATATTGGTGTTGGGACTGGTTGAACAATTTATCCTCCATTATCATCTATTTTGGGACATGGGGGAATTTCAGTTGATTTAGCTATTTTTTCTTTACATATAGCTGGAATTTCTTCAATTATAGGGTCAATTAATTTTATTACAACAATTTTAAATATACGTTTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTATTTGATCTATTTTTATTACAACAATTTTATTATTATTATCTTTACCTGTTTTAGCTGGTGGTATTACAATATTATTGACTGATCGAAATTTAAATACCACATTTTTTGA Atanycolus_sp_GU173827 TATATTATATTTTTTATTTGGTATGTGGTCGGGAATTTTAGGTTTATCTATAAGATTAATTATTCGATTAGAATTGGGGATACCTGGGAGTTTATTAGGAAATGACCAAATTTATAATGGTTTAGTTACATCACATGCTTTTGTTATAATTTTTTTTATGGTTATACCAATTATGGTAGGTGGATTTGGGAATTGATTAATTCCTTTAATATTAGGGGTTCCTGACATAGCTTTCCCACGTATAAATAATATAAGTTTTTGATTATTAATTCCTTCATTAATTTTATTAATTTTAAGAGGATTTGTAAATATTGGTGTTGGGACTGGTTGAACAATTTATCCTCCATTATCATCTATTTTGGGACATGGGGGAATTTCAGTTGATTTAGCTATTTTTTCTTTACATATAGCTGGAATTTCTTCAATTATAGGGTCAATTAATTTTATTACAACAATTTTAAATATACGTTTATTTTTTTTAAAATTAGATCAATTAAGTTTATTTATTTGATCTATTTTTATTACAACAATTTTATTATTATTATCTTTACCTGTTTTAGCTGGTGGTATTACAATATTATTGACTGATCGAAATTTAAATACCACATTTTTTGA Atanycolus_hicoriae_GU173825 AATATTATATTTTTTTTTTGGTATATGATCAGGAATATTAGGTTTATCTATAAGATTAATTATTCGTTTAGAGTTAGGTATACCTGGTAGATTATTAGGAAATGATCAAATTTATAATGGTTTAGTTACATCTCATGCTTTTGTAATGATTTTTTTTATGGTTATACCAATTATAGTAGGTGGATTTGGAAATTGATTAATTCCTTTAATGTTAGGTGTTCCTGATATAGCTTTCCCACGAATAAATAATATAAGTTTTTGATTATTAATTCCTTCATTAATTTTATTAATTTTAAGAGGTTTTGTAAATACTGGTGTTGGAACTGGTTGAACAGTTTATCCTCCATTATCTTCTATTATAGGACATGGGGGAATTTCAGTTGATTTATCTATTTTTTCTTTACATATAGCTGGAATTTCTTCAATTATAGGTTCAATTAACTTTATTACAACAATTTTAAATATGCGTTTATTTTTTTTAAAGTTGGATCAGTTAAGTTTATTTATTTGATCTATTTTTATTACAACAATTTTATTGTTGTTATCTTTACCTGTTTTAGCTGGTGGAATTACAATATTATTAACTGATCGTAATTTAAATACTACATTTTTTG- ; END; BEGIN TREES; Title Set_of_13_MP_Trees_from_analysis_of_COI_data_for_Atanycolus; LINK Taxa = Taxa; TRANSLATE 1 Doryctes_sp_GU173830, 2 Atanycolus_simplex_GU173831, 3 Digonogastra_sp_GU173829, 4 Atanycolus_longifemoralis_J0086, 5 Atanycolus_longifemoralis_J0087, 6 Atanycolus_longifemoralis_J0088, 7 Atanycolus_longifemoralis_J0089, 8 Atanycolus_ulmicola_GU173828, 9 Atanycolus_ulmicola_GU173832, 10 Atanycolus_ulmicola_GU173833, 11 Atanycolus_sp_GU173826, 12 Atanycolus_sp_GU173827, 13 Atanycolus_hicoriae_GU173825; TREE Atanycolus_MP_Tree_1 = (1:13.0,((2:6.0,3:4.0):3.0,((4:0.0,5:0.0,6:0.0,7:0.0):4.0,(8:1.0,9:0.0,10:1.0):3.0):1.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); TREE Atanycolus_MP_Tree_2 = (1:12.0,((2:6.0,((4:0.0,5:0.0,6:0.0,7:0.0):4.0,(8:1.0,9:0.0,10:1.0):3.0):2.0):1.0,3:5.0):3.0,((11:1.0,12:1.0):2.0,13:3.0):3.0); TREE Atanycolus_MP_Tree_3 = (1:13.0,(((2:7.0,3:3.0):3.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0,(8:1.0,9:0.0,10:1.0):3.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); TREE Atanycolus_MP_Tree_4 = (1:14.0,(((2:6.0,3:4.0):3.0,(8:1.0,9:0.0,10:1.0):3.0):1.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):2.0); TREE Atanycolus_MP_Tree_5 = (1:12.0,((((2:6.0,3:4.0):3.0,(8:1.0,9:0.0,10:1.0):3.0):1.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):2.0,13:4.0):2.0,(11:1.0,12:1.0):3.0); TREE Atanycolus_MP_Tree_6 = (1:12.0,(((2:7.0,(8:1.0,9:0.0,10:1.0):3.0):1.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0,3:5.0):3.0,((11:1.0,12:1.0):2.0,13:3.0):3.0); TREE Atanycolus_MP_Tree_7 = (1:12.0,((2:7.0,(4:0.0,5:0.0,6:0.0,7:0.0):5.0,(8:1.0,9:0.0,10:1.0):3.0):1.0,3:6.0):2.0,((11:1.0,12:1.0):2.0,13:3.0):3.0); TREE Atanycolus_MP_Tree_8 = (1:13.0,(2:7.0,(3:6.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0,(8:1.0,9:0.0,10:1.0):3.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); TREE Atanycolus_MP_Tree_9 = (1:13.0,((2:6.0,(3:5.0,(4:0.0,5:0.0,6:0.0,7:0.0):5.0):1.0):1.0,(8:1.0,9:0.0,10:1.0):3.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); TREE Atanycolus_MP_Tree_10 = (1:12.0,(((2:6.0,((8:1.0,9:0.0):1.0,10:0.0):3.0):2.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0,3:5.0):3.0,((11:1.0,12:1.0):2.0,13:3.0):3.0); TREE Atanycolus_MP_Tree_11 = (1:13.0,((2:7.0,(8:1.0,9:0.0,10:1.0):3.0):0.0,(3:6.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); TREE Atanycolus_MP_Tree_12 = (1:14.0,(2:6.0,(((4:0.0,5:0.0,6:0.0,7:0.0):3.0,((11:1.0,12:1.0):3.0,13:2.0):4.0):2.0,(8:1.0,9:0.0,10:1.0):3.0):1.0):1.0,3:5.0); TREE Atanycolus_MP_Tree_13 = (1:13.0,((2:6.0,((8:1.0,9:0.0):1.0,10:0.0):3.0):1.0,(3:6.0,(4:0.0,5:0.0,6:0.0,7:0.0):4.0):1.0):2.0,((11:1.0,12:1.0):3.0,13:2.0):3.0); END; BEGIN CODONS; CODONPOSSET * UNTITLED = N: 1- 615 ; CODONPOSSET CodonPositions = N: 1- 615 ; CODESET * UNTITLED = universal: 1 - 615; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 615; EXSET * UNTITLED = 1 - 168 272 - 615; END; BEGIN MacClade; Version 4.0 87; LastModified -884103331; 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 - 615; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1343935305635; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3053227606447994218; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3109682247354002847; mqVersion 274; checksumv 0 2 12635344 null getNumChars 615 numChars 615 getNumTaxa 13 numTaxa 13 short true bits 15 states 15 sumSquaresStatesOnly 189078.0 sumSquares 189078.0 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 1103 611; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3053227606447994218 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3053227606447994218; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1003 544; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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.ManageTrees.ManageTrees; tell It; showTrees 0 #mesquite.lists.TreesList.TreesList; tell It; setTreeBlock 1; getWindow; tell It; newAssistant #mesquite.lists.NumForTreeList.NumForTreeList; tell It; suppress; setValueTask #mesquite.trees.NumberOfTaxa.NumberOfTaxa; desuppress; endTell; newAssistant #mesquite.lists.TreeListRooted.TreeListRooted; newAssistant #mesquite.lists.TreeListPolys.TreeListPolys; newAssistant #mesquite.lists.TreeListPolyAssumption.TreeListPolyAssumption; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1003 544; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TreesList.TreesListWindow.ibeam; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3053227606447994218 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 895.1328123084342.6643929209318731277; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1003 544; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.interchange; 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 #3109682247354002847 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 373; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1003 544; 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;