#NEXUS [written Mon Mar 11 12:04:56 HST 2013 by Mesquite version 2.75 (build 564) at dhcp-128-171-206-139.stjohn.hawaii.edu/128.171.206.139] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=10; TAXLABELS Fusarium_verticillioides Botrytis_calthae Botrytis_tulipae Botrytis_elliptica Botrytis_galanthina Botrytis_cinerea_B05.10 Botrytis_cinerea_T4 Fusarium_oxysporum Fusarium_fujikuroi Cryphonectria_parasitica ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "phylo_bik4_final.nxs"'; DIMENSIONS NCHAR=990; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Fusarium_verticillioides ATGTCATCTCCACATCTCTCCAAAGTCCTCGTCTTTGGTGCCACCGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCGCTCGGCGCTCACGTCTCCATCGCCCTACGCGACACAACCAAGACCAACGAGTGGATATCCCCCTCCCAAGAACGCGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGATCCCGACTCCCTCAAGCGGGCCGTGCATGACACAGGCGCCCAGGCAGCCTTCATCTACGCCGTGCGC---TCCAAGGACGCGTTGCGTGGTGCCATCGCCGCCCTGCGCGACGCTGGCATCCAGTACGTCGTCTTCCTCTCGACGAGTCAGGTTCGGACCGCGGGCACCACCAAGGGTGACATTCGATCAATCAAACCTGATCACTTTATTCCCTGGCAGCATGCGCAGGTTGAGATTGCGCTGGAGGAGCTC---GAGGTGCCACATGCAGCGGTACGGGCCGGGTTCTTTGCGAGCAACCCGCTAAGAATCTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATCTGCTAGCTCCGGAGGTGCCGCATGATCCCATTGACCCCAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAACCCGCGGCTGTACGCGAGTGGCTATCAGGGGGAGCCCAAGAAGGATGTTGTGTATCTCAGCGGACCGGCGTTGCTCTCGCAGACTGAGCAGTGGGAGATCATTAACCGGGAGCTTGTTGTTGCTGGTAAGCCTGAGGTCAAGGTCAATCACATCACGGTTGAGCAGTACCTTGAAAACCTAGCCAAGCTTCATGTTCCTGATGTTGTAGCCAAGTCTCTTGCCAAGTCTATGGTG---------GAGACGAGGGCACTCTATGCACCTGAGGACTATGAGAAGTCGCGGGGTAACGTTGAGCTCCTGACGGGCCAA--------------------------------------------------- Botrytis_calthae ATGCCATCTCCACATTTCTCCAAAGTCCTTGTCTTTGGTGCCACCGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCTCTCGGCGCCCACATCTTCATTGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGAGCAAGAGCGCGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGACCTGGACTCCGTAAAGCGGGCCGTGCAAGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCCAAGGACACGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTACGTCGTGTTCCTGTCGACCAGTCAGGTCAGGACTGCGGGCACCACAAAGGGTGACATTCGATCCATCAAGCCAGACCATTTCATCCCATGGCAGCATGCGCAGGTCGAGATTGCGCTGGAGGAGCTC---GAGGTGCCACATGCAGCGGTACGGGCCGGGTTCTTTGCGAGCAACCCGCTGCGAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCGGAAGTGCCGCACGATCCCATTGACCCGAAGGATATTGGGCGTGCGGCTGCAGCCATGTTAGTCAACCCGCGGCTGTACGCGAGTGGCTACCAGGGAGAGCCCAAGAAGGACGTTGTTTATCTCAGCGGGCCAGCGTTGCTCTCGCAGACTGAGCAGTGGGAGATTGTTAACCGAGAGCTTGTCGCTGCTGGCAAGCCCGAGGTCAAGATCAATCACATTACCGTCGAGCAGTACCTCGAGAATCTGGCCAAGCTTCATGTTCCCGATATTGTAGCGAAGTCTTTGGCCAAGTCCATGGTG---------GAGACGAGGGCACTGTATGCCCCTGAAGACTATGAGAAGTCGCGGGGTAATGTTGAGCTCTTGACGGGCCGCAAGGCTACATCATTTGATGACTTTGTTAAGAGAGAGATACCAAGATACTTC Botrytis_tulipae ATGCCATCTCCACATTTCTCCAAAGTCCTCGTCTTTGGTGCAACCGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCTCTCGGCGCCCACGTCTCCATCGCCCTACGCGACACAACCAAGCACAACGAGTGGATCTCTCCCTCACAGGAACACGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGATCCCGACTCCCTGAAGCGGGCCGTGCATGACACAGGCGCCCAGGCAGCTTTCATCTACGCCGTTCGA---TCCAAGGACACGTTGCGTGGTGCCATCACGGCCCTGCGCGACGCTGGCATCCAGTACCTCGTCTTCCTGTCGACGAGTCAGGTTAGGACCGCGGGCACCACCAAGGGTGACATTCGATCCATCAAGCCTGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAGATTGCGCTGGAGGAGCTT---GAGGTGCCACATGCAGCGGTCCGGGGCGGGTTCTTTGCGAGCAACCCGCTAAGAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCGGAAGTGCCGCATGATCCCATTGACCCCAAGGATATTGGGCGTGCGGCTGCTGCCGTCTTAGTCAACCCGCGGCTGTATGCGAGTGGCTATCAGGGAGAGCCAAAGAAGGACGTCGTTTATCTAAGCGGACCGGCCTTGCTCTCGCAGACTGAGCAGTGGGAGATTATCAACCGGGAGCTTGTCGCTGCAGGTAAGCCTGAGGTCAAGGTCAATCACATTACGGTTGAGCAATACCTTGAGAATCTGGCCAAGCTCCATGTTCCTGATGTTGTAGCCAAGTCTCTTGCTAAGTCCATGGTT---------GAGACGAGGGCACTGTATGCTCCTGAGGATTACGAGAAGTCGCGGGGTAATGTTGAGCTTTTGACAGGCCGCAAGGCTACAGCATTTGATGAATTTGTCAAGAGAGAGATACCAAGATACTTT Botrytis_elliptica ATGTCATCTCCACATTTCTCCAAAGTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCTCTCGGCGCCCACGTCTTCATCGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGATCAAGAGCGCGCCGCAGATCTGCAGCGCACCAGTGCCGACTTAACCGACCTGGACTCTGTGAAGCAGGCCGTGCACGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCCAAGGACACGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGATCAGGACCGCGGGCACCACAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAGATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCGGGCTTCTTTGCGAGCAACCCGCTGCGAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCAGAAGTGCCGCACGATCCCATTGACCCGAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAGTCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTTGTGTATCTTAGTGGACCAGCTTTGCTCTCTCAGACTTTGCAGTGGGAGATCATCAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCAAGGTGAATCATATCACGGTTGAGCAGTACCTTGAGAATCTGGCCAAGCTTCATGTTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCTGAGGACTATGAGAAGTCCCGGGGTAACGTTGAGCTCTTGACAGTCCGCAAAGCTACATCATTTGACGACTTTGTTAAGAGAGAGATACCAAGGTACTTC Botrytis_galanthina ATGTCATCTCCACATTTCTCCAAAGTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCTCTCGGCGCCCACGTCTTCATCGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGATCAAGAGCGCGCCGCAGATCTGCAGCGCACCAGTGCCGACTTAACCGACCTGGACTCTGTGAAGCAGGCCGTGCACGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCCAAGGACACGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGATCAGGACCGCGGGCACCACAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAGATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCGGGCTTCTTTGCGAGCAACCCGCTGCGAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCAGAAGTGCCGCACGATCCCATTGACCCGAAGTATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAGTCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTTGTGTATCTTAGTGGACCAGCTTTGCTCTCTCAGACTTTGCAGTGGGAGATCATCAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCAAGGTGAATCATATCACGGTTGAGCAGTACCTTGAGAATCTGGCCAAGCTTCATGTTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCTGAGGACTATGAGAAGTCCCGGGGTAACGTTGAGCTCTTGACAGTCCGCAAAGCTACATCATTTGACGACTTTGTTAAGAGAGAGATACCAAGGTACTTC Botrytis_cinerea_B05.10 ATGTCATCTCCATATTTCTCCAAAGTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACACTCTCGGCGCCCACGTCTTCATCGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGATCAAGAGCGTGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGGCCTGGACTCTGTGAAGCAGGCCGTGCACCAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCCAAGGACACGTTGCGTGGTGCTATTATCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGGTCAGGACCGCGGGCACCATAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCAAGGCAGCATGCGCAGGTCGAGATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCCGGCTTCTTTGCGAGCAACCCGCTGTTAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCGATTTGCTAGCTCCAGAAGTGCCGCACGATCCCATTGACCCGAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTTAGCCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTAGTGTATCTCAGTGGACCAGCTTTGCTCTCCCAGACTGTGCAGTGGGAGATCACCAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCAAGGTGAATCATATCACGGCTGAGCAGTACCTTGAGAATCTGGCCAAGCTTCATGCTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCCGAGGACTATGAGAAGTCCCGGGGTAACGTTGAGCACTTGACAGGCCGCAAGGCTACATCATTTGATGACTTTGTTAAGAGAGAGATACCAAGGTACTTC Botrytis_cinerea_T4 ATGTCATCTCCACATTTCTCCAAATTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGTCCACGCTCTCGGCGCCCACGTCTTCATCGCCCTACGCGACACATCCAAGCACAATGAGTGGATCTCGCCCGATCAAGAGCGCGCCGCAGGTCTGCAGCGCATCAGTGCCGACCTAACCGACCTGGACTCTGTGAAGCAGGCCGTGCACGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCTAAGGACACGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGGTCAGGACCGCCGGCACCATAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAAATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCCGGCTTCTTTGCGAGCAACCCGCTGCGAATTTACCTCGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCAGAAGTGCCGCACGATCCCATTGATCCGAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAGCCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTTGTGTATCTCAGTGGACCAGCCTTGCTCTCCCAGACTGTGCAGTGGGAGATCATCAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCAAGGTGAATCATATCACGGTTGAGCAGTACCTTGAGAATCTGGCCAAGCTTCATGTTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCTGGGGACTATGAGAAGTTCCGGGGTAACTTTGGGCTCTTGACAGGCCGCAAGGCTACATCATTTGATGACTTTGTTAAGAGAGAGATAACAAGGTACTTC Fusarium_oxysporum ATGTCATCTCCACATTTTTCAAAAGTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGTCCACGCTCTCGGCGCCCAAGTCTTCATCGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGATCAAGAGCGCGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGACCTGGACTCTGTGAAGCAGGCCGTGCACGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCGC---TCCAAGGACACGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGGTCAGGACCGCGGGCACCACAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAGATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCCGGCTTCTTTGCGAGCAACCCGCTGCGAATTTACCTTGATCGATCTTCAGAGCCTAAACAAGTCCATCTGCTAGCTCCAGAAGTGCTGCACGATCCCATTGACCCGAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAGCCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTTGTGTACCTCAGTGGACCAGCTTTGCTCTCCCAGACTGTGCAGTGGGAGATCATAAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCGAGGTGAATCATATCACGGTTGAGCAGTACCTTGAGAATCTGGCCAAGCTTCATGTTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCTGAGGACTATGAGAAGTCCCGGGGTAACGTTGAGCTCTTGACAGGCCGCAAGGCTACATCATTTGATGACTTTGTTAAGAGAGAGATACCAAGGTACTTC Fusarium_fujikuroi ATGTCATCTCCACATTTCTCCAAAGTCCTTGTCTTTGGTGCCACTGGCGAAGTTGGCTCCGCCGTCGCACTCGAGGCCCACGCTCTCGGTGCCCACGTCTTCATCGCCCTACGCGACACATCCAAGCACAACGAGTGGATCTCGCCCGATCAAGAGCGCGCCGCAGACCTGCAGCGCATCAGTGCCGACCTAACCGACCTGGACTCTGTGAAGCGGGCCGTGCACGAGACAGGCGCCCAGGCTGCCTTCATCTACGCCGTGCAC---TCCAAGGATATGTTGCGTGGTGCCATTACCGCCCTGCGCGACGCTGGCATCCAGTATGTCGTGTTCCTGTCGACCAGTCAGGTCAGGACCACGGGCACCACAAAGGGTGACATTCGATCCATCAAGCCAGACCACTTCATCCCATGGCAGCATGCGCAGGTTGAGATTGCGCTGGAAGAACTC---GAGGTGCCACATGCAGCGGTACGGGCCGGCTTCTTTGCGAGCAACCCGCTGCGAATTTACCTTGATCGATCTTCGGAGCCTAAACAAGTCAATTTGCTAGCTCCAGAAGTGCCGCACGATCCCATTGACCCGAAGGATATTGGGCGTGCGGCTGCTGCCGTGTTAGTCAGCCCGCGGCTGTACGCGAGTGGCTATCAAGGAGACCCCAAGAAGGATGTTGTGTATCTCAGTGGACCAGCTTTGCTCTCCCAGACTGTGCAGTGGGAGATTATCAACCGAGAGCTTGTTGCTGCTGGTAAGCCTGAAGTCAAGGTGAATCATATCACGGTTGAGCAGTACCTTGAGAATCTGGCCAAGGTTCATGTTCCTGACGTGGTCGCCAAGTCTCTAGCCAAGTCCATGGTG---------GAGACGAGGGCACTATATGCTCCTGAGGACTATGAGAAGTCCCGGGGTAACGTTGAGCTCTTGACAGGCCGCAAGGCTACACCATTTGATGACTTTGTTAAGAGAGAGATACCAAGGTACTTC Cryphonectria_parasitica ATGTCTTCCCGCAAGTACAACAACGTAATCGTCTTTGGCCCTACTGGCGGTGTGGGCTCTCAGGTCGCCCTCGAAGCCAACAGGCGCGGAGCCAAGGTGTGGCTCGCGATGCGGGACCCTACCAAGACCATTCAAGACATCCCCGCCGATGTTGAGAAGTCCGGCAACTTCGCCCGTATCCAGGCCGACCTCACAGACCCG---------------------------------------GCCGCGTACATCTACTTGATCCACGGGGCGTCGGATGGCATGCGTGGAGCGCTACAAGCGCTGCGCGATGCTGGCGTCGAGAGCGTTGTCTTTCTGTCAAGCTTCTCGATCACACCGGCT------------CATGAACTCCGCAAGATCCCACAGTCGGCCTTCATTCCCTGGCTCCACGCCCAAGTCGAGATCGCGGCGGAGGAGGTGGGCATACCCTACTTCACGGCGCTGCGGCCCGCCGCATTCGCCAGCAATCACTTCAAGAACTTCCTCGACCGGTCTGCGAAGCCACCCAGGGCGACGCATATCCGGGACGACGCCTGGGTCGACAACATCACTCCGGAGGATATGGGCGCGGTGGGGGCCGCCGTGCTCGTGGAGAGGCCTTCG------------------------AACGGAACCGAGATCATCTACCTGGCCGGACCGGAGCTGATCACCAAGGCGCAGAGCTGGGAAATCATCAAGAAG---------ATCACCGGTCGTCACGACATCAACGCGAACCCTATCACCAAGGAGGAATTCCTCAAGCAGGCTCAGGCCCATCATCTCCCAACTAAGGTCGCAGAGTACCTGGTCACGGTCGACGATGAATCAACCGAGCGTTCCTACCTCTTCTCAGAAGCCTTGCACCGTGAATCCGTCGCAAACATCAAGAAGTACTCTGGCAAGGAGCCACTCGGATTTGCAGAGTATATCGAGGCGCACAAGGCAGAGTGGCAG ; END; BEGIN TREES; Title 'Trees from "phylo_bik4_final.nxs"'; LINK Taxa = Taxa; TRANSLATE 1 Fusarium_verticillioides, 2 Botrytis_calthae, 3 Botrytis_tulipae, 4 Botrytis_elliptica, 5 Botrytis_galanthina, 6 Botrytis_cinerea_B05.10, 7 Botrytis_cinerea_T4, 8 Fusarium_oxysporum, 9 Fusarium_fujikuroi, 10 Cryphonectria_parasitica; TREE tree_1 = ((1:0.020456889322189253,(((2:0.008283277109414344,(3:0.02416656029922626,((4:0.011825397156781214,5:0.01920860572571126):0.0011587693025715273,(6:1.047332781722865E-6,7:0.0011533649844035487):0.014286457783071027):1.047332781722865E-6):0.0022797329139492284):0.03559877209361195,8:0.037000941476984406):0.03647962475582123,9:0.03829374032693489):0.031655784791522645):0.5333506138321209,10:0.5333506138321209); END; BEGIN MacClade; Version 4.0 87; LastModified -849119044; FileSettings editor '0' '0' '1' '1'; Singles 000; Editor 11011001111111100100010010 '1' '12' Geneva '9' '100' '1' all; EditorPosition '44' '6' '707' '1203'; TreeWindowPosition '46' '6' '735' '1230'; ListWindow Characters closed Geneva '9' '50' '10' '129' '399' 000; ListWindow Taxa closed Geneva '9' '50' '10' '129' '365' 100000000; ListWindow Trees closed Geneva '9' '50' '10' '129' '379'; 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' '25' '129' '181'; 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' '718' '1220'; StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220'; WindowOrder Data; OtherSymbols & / 00 ? -; Correlation '0' '0' '1000' '0' '0' 10011010; Salmo 00000001; EditorFile '2'; ExportHTML _ MOSS '100' 110000; PrettyPrint 10; EditorToolsPosition '593' '46' '115' '165'; TreeToolsPosition '620' '9' '126' '138'; TreeWindowProgram 10; TreeWindow 0000; Continuous '0' '3' 1; Calculations 0000001; SummaryMode '0' '0' 0; Charts Geneva '9' ( normal ) 0010; NexusOptions '0' '0' '50' 001011011; 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' '-12473' '-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 ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 990; END; BEGIN CODONS; CODONPOSSET * UNTITLED = 1: 1 - 988\3, 2: 2 - 989\3, 3: 3 - 990\3; CODONPOSSET CodonPositions = 1: 1 - 988\3, 2: 2 - 989\3, 3: 3 - 990\3; CODESET * UNTITLED = universal: 1 - 990; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 990; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1363039497355; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3634589244940620230; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5185058682130927682; mqVersion 275; checksumv 0 3 4125603702 null getNumChars 990 numChars 990 getNumTaxa 10 numTaxa 10 short true bits 15 states 15 sumSquaresStatesOnly 186723.0 sumSquares 186723.0 longCompressibleToShort false usingShortMatrix true 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 1503 211; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3634589244940620230 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3634589244940620230; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 1503 211; 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 #3634589244940620230 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 2355.1363039489617.1130709752403493009; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 1503 211; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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 #5185058682130927682 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 600 397; setLocation 1503 211; 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.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;