#NEXUS [written Wed Jun 23 14:40:23 EDT 2010 by Mesquite version 2.72 (build 528) at fre1/140.232.239.134] BEGIN TAXA; TITLE Volvopluteus; DIMENSIONS NTAX=11; TAXLABELS Pluteus_longistriatus_Minnis309203_Missouri Pluteus_heteromarginatus_AJ172_Florida Volvopluteus_gloiocephalus_AJ239_Spain Volvopluteus_gloiocephalus__LOU13710_Spain Volvopluteus_gloiocephalus__LOU18247_Spain Volvopluteus_gloiocephalus__PBM2272_California Volvopluteus_gloiocephalus__LOU18619_Portugal Volvopluteus_earlei_MA22816_Spain Volvopluteus_earlei_Mamet7_Congo Volvopluteus_asiaticus_TNSF15191_Japan Volvopluteus_michiganensi_Smith32590_Michigan ; END; BEGIN CHARACTERS; TITLE Volvopluteus; DIMENSIONS NCHAR=655; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Pluteus_longistriatus_Minnis309203_Missouri CCTGCGGAAGGATCATTATTGAACAAACC??GGTG?TGGCTG???AGCTGGCCTTTTC????????---GAAGG--------CATGTGCACGGCCCGCCATT-GTTTCATCC?????TTCTCTTCCACCTGTGCAC?TTCTGTGGG??CCC???????---TGCGCTGGAACCTGGTGCCTACGTTT-CACTA-TCTACACC-ATT-?GAATGT??TCAGAATGCA?TGAA-TTGGGCGTTACTGCCTA-TAAAACCTT?ATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAAATC-ATCAACC???ACCT??CATCTT????TG????AGA?GGGTTGGA-CTTGGAGGTGCTGGCCCTCTCCGGGACCCGGCTCCTCTGAAAAGCATTAGCAGGGGCTCATCCTGTGCGATCTGCAGCCTTGTGTGATAGT?TATC??TACACT???CGGCGCGGT???CACATTCACCCAGCTTACAGCCGTCTGCCAG????CGCGGACAACTTATT?????????TGACCA Pluteus_heteromarginatus_AJ172_Florida CCTGCGGAAGGATCATTATTGAACAAACC??GGCGTTGGCTG???AGCTGGCCTTTTC????????---GGAGG--------CATGTGCACGGCCCGCCATT?GTTTCATCC?????TTCTCTTCCACCTGTGCAC?TTCTGTGGG??CCC???????---TGC--TGGACTCTGGTGCCTACGTCT-CACTA-CCTACACC-ATT-?GAATGT??TCAGAGCGCA?TGAA-TAGGGCATTCTTGCCTA-TAAAACCTTAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGCATTCCGAGGAGCATGCCTGTTTGAGTGTCATTAAATC-ATCAACC???ACCT??CATCTT????TG????AGA?GGGTTGGA-CTTGGAGGTGCTGGCCCTCTCCGGGA?TCGGCTCCTCTGAAAAGCATTAGCAGGGGCTCATATTGTGCATTCTGCAGCCTTGTGTGATAGT?CATC??TACACT???CGGCGCGGT???CACATTCACCCAGCTTCCAGCCGTCCG????????CTCGGACAAC??ATC?????????TGACCA Volvopluteus_gloiocephalus_AJ239_Spain CCTGCGGAAGGATCATTATTGAATAAACCATGGCG??GGCAGTCTTGCTGGCCTTTTCCCTCCTCC-AGGGAGGAGAGAGGGCATGTGCACGCTCGTCAAAA?GTTTCATTCGCATACCCCTTTCCACCTGTGCACACACTGTAGG??TCCCGTTAGAA?-CCTCCCCTTTTTCGGA-CCTACGTTTT-ACAACCCTACCCC--CT-CGAATATGATACGAACGTAGTGA-CTTGGGCCACCGCGCCTAATAAAA-CATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAGCT???CCCCTCCAGTTTTGTCTGGTA?GGATGGGTTGGATCATGGGGGTGTCGGCTCCATTGCGAA?TCGACTCCCCTGAAAAGCATTAGTAG????????TCCGTGCTGTCTGCCGCC?GGTGTGATAAT?AATCTTTATGCCGCCTGGTCCAGCATACACG?TTG?TCTGCTCCAAACAGTCCGAGCACAATCTCGGACATC??ACAATTTTATTTTGACCA Volvopluteus_gloiocephalus__LOU13710_Spain CCTGCGGAAGGATCATTATTGAATAAACCATGGCG??GGCAGTCTTGCTGGCCTTTTCCCTCCTCC-AGGGAGGAGAGAGGGCATGTGCACGCTCGTCAAAA?GTTTCATTCGCATACCCCTTTCCACCTGTGCACACACTGTAGG??TCCCGTTAGAA?-CCTCCCCTTTTTCGGA-CCTACGTTTT-ACAACCCTACCCC--CT-CGAATATGATACGAACGTAGTGA-CTTGGGCCACCGCGCCTAATAAAA-CATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAGCT???CCCCTCCAGTTTTGTCTGGTA?GGATGGGTTGGATCATGGGGGTGTCGGCTCCATTGCGAA?TCGACTCCCCTGAAAAGCATTAGTAG????????TCCGTGCTGTCTGCCGCC?GGTGTGATAAT?AATCTTTATGCCGCCTGGTCCAGCATACACG?TTG?TCTGCTCCAAACAGTCCGAGCACAATCTCGGACATC??ACAATTTTATTTTGACCA Volvopluteus_gloiocephalus__LOU18247_Spain CCTGCGGAAGGATCATTATTGAATAAACCATGGCG??GGCAGTCTTGCTGGCCTTTTCCCTCCTCC-AGGGAGGAGAGAGGGCATGTGCACGCTCGTCAAAA?GTTTCATTCGCATACCCCTTTCCACCTGTGCACACACTGTAGG??TCCCGTTAGAA?-CCTCCCCTTTTTCGGA-CCTACGTTTT-ACAACCCTACCCC--CT-CGAATATGATACGAACGTAGTGA-CTTGGGCCACCGCGCCTAATAAAA-CATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAGCT???CCCCTCCAGTTTTGTCTGGTA?GGATGGGTTGGATCATGGGGGTGTCGGCTCCATTGCGAA?TCGACTCCCCTGAAAAGCATTAGTAG????????TCCGTGCTGTCTGCCGCC?GGTGTGATAAT?AATCTTTATGCCGCCTGGTCCAGCATACACG?TTG?TCTGCTCCAAACAGTCCGAGCACAATCTCGGACATC??ACAATTTTATTTTGACCA Volvopluteus_gloiocephalus__PBM2272_California CCTGCGGAAGGATCATTATTGAATAAACCATGGCG??GGCAGTCTTGCTGGCCTTTTCCCTCCTCC-AGGGAGGAGAGAGGGCATGTGCACGCTCGTCAAAA?GTTTCATTCGCATACCCCTTTCCACCTGTGCACACACTGTAGG??TCCTGTTAGAA?-CCTCCCCTTTTTCGGA-CCTACGTTTT-ACAACCCTACCCC--CT-CGAATATGATACGAACGTAGTGA-CTTGGGCCACCGCGCCTAATAAAA-CATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAGCT???CCCCTCCAGTTTTGTCTGGTA?GGATGGGTTGGATCATGGGGGTGTCGGCTCCATTGCGAA?TCGACTCCCCTGAAAAGCATTAGTAG????????TCCGTGCTGTCTGCCGCC?GGTGTGATAAT?AATCTTTATGCCGCCTGGTCCAGCATACACG?TTG?TCTGCTCCAAACAGTCCGAGCACAATCTCGGACATC??ACAATTTTATTTTGACCA Volvopluteus_gloiocephalus__LOU18619_Portugal CCTGCGGAAGGATCATTATTGAATAAACCATGGCG??GGCAGTCTTGCTGGCCTTTTCCCTCCTCC-AGGGAGGAGAGAGGGCATGTGCACGCTCGTCAAAA?GTTTCATTCGCATACCCCTTTCCACCTGTGCACACACTGTAGG??TCCCGTTAGAAG-CCTCCCCTTTTTCGGA-CCTACGTTTT-ACAACCCTACCCC--CT-CGAATATGATACGAACGTAGTGA-CTTGGGCCACCGCGCCTAATAAAA-CATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAGCT???CCCCTCCAGTTTTGTCTGGTA?GGATGGGTTGGATCATGGGGGTGTCGGCTCCATTGCGAA?TCGACTCCCCTGAAAAGCATTAGTAG????????TCCGTGCTGTCTGCCGCC?GGTGTGATAAT?AATCTTTATGCCGCCTGGTCCAGCATACACG?TTG?TCTGCTCCAAACAGTCCGAGCACAATCTCGGACATC??ACAATTTTATTTTGACCA Volvopluteus_earlei_MA22816_Spain CCTGCGGAAGGATCATTATTGGATAAACCAAGGCG??AGCTGTCTTGCTGGCC---TCCC-?CTCC-----AGGAGG-----CATGTGCACGCCCGTCAAAC?GTTTCATTC????ATCCCTTTCCACCTGTGCACACACTGTAGG??T--CG??-GAAA-GGC--CTCCTTCCGGT-CCTACGTCT-CACAT-CCTACCCCA-CTACAAATGTGATACGAATGTAACGATCTA-GGCCTCCGCGCCTAAT?AAA-CACAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAACT???-CCCTCCAG?TTTGTCTGGTAGGGGCCG-TTGGATCTTGGGGGTGTCGGCTC??TTGTGGG?TCGACTCCCCTGAAAAGCATTAGCAG????????T?CGTGCTGTCTGCCGCC?GGTGTGATAGT?TATC??TATGCCGTCTGGTCCAGCGTATGCG?TTG?TCTGCTCCGAACAGTCCGAACA????GTCGGACAAC??ACAAAT??????TGACCA Volvopluteus_earlei_Mamet7_Congo CCTGCGGAAGGATCATTATTGGATAAACCAAGGCG??AGCTGTCTTGCTGGCC---TCCC-?CTCC-----AGGAGG-----CATGTGCACGCCCGTCAAAC?GTTTCATTC????ATCCCTTTCCACCTGTGCACACACTGTAGG??T--CG??-GAAA-GGC--CTCCTTCCGGT-CCTACGTCT-CACAT-CCTACCCCA-CTACGAATGTGATACGAATGTAACGATCTA-GGCCTCCGCGCCTAAT?AAA-CACAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAACT???-CCCTCCAG?TTTGTCTGGTAGGGGCCG-TTGGATCTTGGGGGTGTCGGCTC??TTGTGGG?TCGACTCCCCTGAAAAGCATTAGCAG????????T?CGTGCTGTCTGCCGCC?GGTGTGATAGT?TATC??TATGCCGTCTGGTCCAGCGTATGCG?TTG?TCTGCTCCGAACAGTCCGAACA????GTCGGACAAC??ACAAAT??????TGACCA Volvopluteus_asiaticus_TNSF15191_Japan CCTGCGGAAGGATCATTATTGAATAAACCATGGTG??GGCTGTCTTGCTGGCC---TCCC-?CTACAA-GGAGG--------TATGTGCACGCCCATCAACCGGTTTCTTTC????ACCCTTCTCCACCTGTGCACACACTGTAGGGATCCCG??-GAAG-GGCTTC-CCTTCTGGACCTTACGTTT-TACAA-CCTACCCCA-CTACGAATGTGATATGAATGTAATTATCTA-GGCCAACGTGCCTATT?AAA-TATAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAACCTTTCCCTTCTAGTTTTGTCTGGTAGGGATGGGTTGGATCTTGGGGGTGTCGGCTCCATTGTGTAACCGACTCCCCTGAAAAGCATTAGCAG????????T?CGTGCTGTCTGCCACC?GGTGTGATAGTAAATC??TATGCCGTCTGGTCCAGTATATGCG?TTG?TCTGCTCCAAATAGTCCAAACA??GTCTTGGACAAC??AATAATTAA???TGACCA Volvopluteus_michiganensi_Smith32590_Michigan ?????????GGATCATTATTGAATAAACCATGGCG??GGCTGTCTTGCTGGCC---TCCC-?CTCCAAGGGAGG--------CATGTGCACGCCCGTCAAAC?GTTTCATTC????ACCCTTCTCCACCTGTGCACACACTGTAGGGATCCTG??-GAAGGGGCTCCTCCTTCCGGACCCTACGTTT-CATTA-CCTACCCCAACTACGAATGTGATACGAATGTAACTATCTA-GGCCACCGTGCCTAAT-AAA-CACAATACAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCAT-AAATCTCTCAACCT?TCCCTTCTGGTTTTTCCTGGTAGGGATGGGTTGGATCTTGGGGGTGTCGGCTCCATTGCGGGTCCGACTCCCCTGAAAAGCATTAGCAG????????T?CGCGCTGTCTGCCACC?GGTGTGATAGT?AATC??TATGCCGTCTGGTCCAGTGTACGCGCTTG?TCTGCTCCGAACAGTCCGAACA??CTCTCGGACAAC??AGTAA?AAA???TGACCA ; END; BEGIN TREES; Title 'Volvopluteus_Consensus_Majrule'; LINK Taxa = Volvopluteus; TRANSLATE 1 Pluteus_longistriatus_Minnis309203_Missouri, 2 Pluteus_heteromarginatus_AJ172_Florida, 3 Volvopluteus_gloiocephalus_AJ239_Spain, 4 Volvopluteus_gloiocephalus__LOU13710_Spain, 5 Volvopluteus_gloiocephalus__LOU18247_Spain, 6 Volvopluteus_gloiocephalus__PBM2272_California, 7 Volvopluteus_gloiocephalus__LOU18619_Portugal, 8 Volvopluteus_earlei_MA22816_Spain, 9 Volvopluteus_earlei_Mamet7_Congo, 10 Volvopluteus_asiaticus_TNSF15191_Japan, 11 Volvopluteus_michiganensi_Smith32590_Michigan; TREE MajRule = (1,2,(((3,4,5,6,7),(8,9)),(10,11))); END; BEGIN PAUP; OUTGROUP Pluteus_longistriatus_Minnis309203_Missouri Pluteus_sp_AJ172_Florida; SET CRITERION = PARSIMONY MAXTREES = 1000 INCREASE = AUTO; HSEARCH ADDSEQ = RANDOM NREPS = 1000 SWAP = TBR NCHUCK = 2 CHUCKSCORE = 1; ROOTTREES ROOTMETHOD = OUTGROUP; SAVETREES FILE = Pluteus_Analysis.tre BRLENS = yes; CONTREE / TREEFILE = Pluteus_Consensus_Strict.tre; CONTREE / STRICT = no MAJRULE = yes TREEFILE = Pluteus_Consensus_Majrule.tree; LOG FILE = Pluteus_PBS.log; BOOTSTRAP TREEFILE = Pluteus_PBS.out NREPS = 1000 CONLEVEL = 50 SEARCH = heuristic / ADDSEQ = random NREPS = 10 SWAP = spr; SAVETREES FILE = Pluteus_bootstrap.tree FORMAT = Nexus APPEND = no REPLACE = yes; LOG STOP; BEGIN CODONS; CODONPOSSET * CodonPositions = N : 1 -655; CODESET * UNTITLED = Universal : all; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 655; END; BEGIN MacClade; Version 4.0 87; LastModified -944581417; FileSettings editor '0' '0' '1' '1'; Singles 100; Editor 00011001111111100100010010 '1' '12' Geneva '9' '198' '1' all; EditorPosition '44' '6' '867' '1493'; TreeWindowPosition '46' '6' '989' '1630'; ListWindow Characters closed Geneva '9' '50' '10' '273' '399' 000; ListWindow Taxa closed Geneva '9' '50' '25' '241' '452' 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' '968' '1620'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder Data; OtherSymbols & / 10 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '753' '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' '100' 001011001; 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' '-25001' '-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' 100010111110111; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1011; BothTools '1'; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 655; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 655; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1277318423346; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3670028765083816623; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 6532174888758109849; checksumv 0 2 2769116693 null getNumChars 655 numChars 655 getNumTaxa 11 numTaxa 11 short true bits 15 states 15 sumSquaresStatesOnly 145220.0 sumSquares 145220.0 NumFiles 1 NumMatrices 1; endTell; getWindow; tell It; suppress; setResourcesState false false 339; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1280 694; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3670028765083816623 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3670028765083816623; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 941 627; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; setActive; 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 #3670028765083816623 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1359.1276266490538.8222057317781697560; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 941 627; setLocation -8 0; 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.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #6532174888758109849 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 256; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 941 627; setLocation -8 0; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; 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; 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.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;