#NEXUS [written Sun Jul 27 16:44:27 CDT 2014 by Mesquite version 2.75 (build 564) at rachel-coburns-macbook-pro.local/10.0.1.17] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=7; TAXLABELS Petunia_hybrida_D14588 Nicotiana_benthamiana_V0.4.2.Scf45423 Solanum_lycopersicum_SL2.40sc03876 Solanum_tuberosum_AY675558 Iochroma_cyaneum_KJ094354 Iochroma_calycinum_KJ094346 Iochroma_calycinum_KJ094345 ; END; BEGIN CHARACTERS; TITLE 'F3_5_H Alignment'; DIMENSIONS NCHAR=1549; FORMAT DATATYPE = DNA GAP = - MISSING = ?; CHARSTATELABELS 333 i, 334 i, 909 i, 910 i ; MATRIX Petunia_hybrida_D14588 ATGATGCTACTTACT------GAGCTTGGT---GCAGCAACTTCAATCTTTCTAATAGCACACATAATCATTTCAACTCTTATTTCAAAAACT------ACCGGCCGGCAT------CTACCGCCGGGGCCAAGAGGGTGGCCGGTGATCGGAGCACTTCCACTTTTAGGAGCCATGCCACATGTTTCCTTAGCTAAAATGGCAAAAAAATATGGAGCAATCATGTATCTCAAAGTTGGAACATGTGGCATGGCAGTTGCTTCTACCCCTGATGCTGCTAAAGCATTCTTGAAAACACTTGATATCAACTTCTCCAATCGTCCACCTAATGCAGGTGCCACTCACTTAGCTTATAATGCTCAAGACATGGTTTTTGCACATTATGGACCACGATGGAAGTTGCTAAGGAAATTAAGCAACTTGCATATGCTAGGGGGAAAAGCCTTAGAGAATTGGGCAAATGTTCGTGCCAATGAGCTAGGGCACATGCTAAAATCAATGTCCGATATGAGTCGAGAGGGCCAGAGGGTTGTGGTGGCGGAGATGTTGACATTTGCCATGGCCAATATGATCGGACAAGTGATGCTAAGCAAAAGAGTATTTGTAGATAAAGGTGTTGAGGTAAATGAATTTAAGGACATGGTTGTAGAGTTAATGACAATAGCAGGGTATTTCAACATTGGTGATTTTATTCCTTGTTTAGCTTGGATGGATTTACAAGGGATAGAAAAACGAATGAAACGTTTACATAAGAAGTTTGATGCTTTATTGACAAAGATGTTTGATGAACACAAAGCAACTACCTATGAACGTAAGGGGAAACCAGATTTTCTTGATGTTGTTATGGAAAATGGGGACAATTCTGAAGGAGAAAGACTCAGTACAACCAACATCAAAGCACTTTTGCTGAATTTGTTCACAGCTGGTACGGACACTTCTTCTAGTGCAATAGAATGGGCACTTGCAGAAATGATGAAGAACCCTGCCATTTTGAAAAAAGCACAAGCAGAAATGGATCAAGTCATTGGAAGAAATAGGCGTTTACTCGAATCCGATATCCCAAATCTCCCTTACCTCCGAGCAATTTGCAAAGAAACATTTCGAAAACACCCTTCTACACCATTAAATCTTCCTAGGATCTCGAACGAACCATGCATAGTCGATGGTTATTACATACCAAAAAACACTAGGCTTAGTGTTAACATATGGGCAATTGGAAGAGATCCCCAAGTTTGGGAAAATCCACTAGAGTTTAATCCCGAAAGATTCTTGAGTGGAAGAAACTCCAAGATTGATCCTCGAGGGAACGATTTTGAATTGATACCATTTGGTGCTGGACGAAGAATTTGTGCAGGAACAAGAATGGGAATTGTAATGGTGGAATATATATTAGGAACTTTGGTTCATTCATTTGATTGGAAATTACCAAGTGAAGTTATTGAGTTGAATATGGAAGAAGCTTTTGGCTTAGCTTTGCAGAAAGCTGTCCCTCTTGAAGCTATGGTTACTCCAAGGTTACAATTGGATGTTTAT---GTACCATAGCTA- Nicotiana_benthamiana_V0.4.2.Scf45423 ATGGTACCATTTACT------GACCTTACTACAGCAGCT---ACAATTTTCCTTATATCACATATTCTCATTTCAATTCTTCTTTCAAAAACT------ACCCGGCGCCGCTGT---CTCCCGCCGGGCCCAAGGGGGTGGCCGGTGATCGGCGCACTACCATACTTAGGAGCCATGCCACATGTTTCACTTGCAAAAATGGCCAAAAAATATGGACCTGTTATGTATTTAAAAGTTGGCACATGTGGTATGGCTGTTGCTTCTACTCCTGATGCTGCTAAAGCATTCTTGAAAACACTTGATATCAACTTCTCCAATCGTCCACCTAATGCAGGTGCCACGCACTTGGCCTATGATGCACAAGACATGGTTTTTGCACATTATGGACCACGTTGGAAGTTGCTAAGGAAATTGAGCAACTTGCATATGCTAGGGGGAAAAGCCTTAGAAAATTGGGCAAATGTACGTGCCAATGAGCTAGGGCACATGCTAAAATCGATGTTCGAAATGAGCCGAGAAGGCGAGCGAGTGGTGCTGGCGGAGATGCTGACATTCGCTATGGCGAATATGATAGGACAAGTGATATTAAGCAAGAGAGTTTTCACGAAAAAAGGTGCTGAGGTTAATGAATTTAAGGATATGGTGGTAGAGTTAATGACAGTAGCAGGGTATTTTAACATTGGAGATTTTATTCCTTCATTAGCTTGGTTGGATTTACAAGGGATTGAAAGTGGGATGAAGAATTTACACAAGAAATTTGATGCTTTGTTGACAAAGATGTTTGATGAACACAAGGAAACTAGCTATGAACGTAAAGGGAAAGAGGATTTTCTTGATGTTGTTATGGCAAATAGGGATAATTCTCAAGGAGAAACGCTCAGTACTACTAATATCAAAGCACTTTTGCTGAATTTGTTCACTGCTGGTACAGACACTTCTTCTAGTGTAATAGAATGGGCACTTGCTGAAATGATGAAAAATCCAAAAATTCTCAAAAAAGCACAAGCAGAAATGGATCAAGTCATTGGAAAAGATAGACGTTTACTTGAATCGGATATCCCAAATCTTCCTTATCTTCGAGCAATTTGCAAAGAAACATTTCGAAAACATCCATCTACACCATTAAATCTCCCCAGAATCTCGAACGAACCATGTGAAGTGAATGGTTATTACATACCAAAAAATACTAGGCTCAGTGTTAATATTTGGGCGATTGGAAGAGACCCTGATGTGTGGGAAAAACCGCTAGAATTTAATCCTGAAAGGTTCTTGAGTGGGAAAAATACAAAGATTGATCCACGAGGGAATGACTTTGAGCTAATTCCATTTGGTGCAGGACGGAGAATTTGTGCAGGAACAAGAATGGGAATAGTAATGGTGGAATATATATTGGGAACTTTGGTTCATTCATTTAATTGGAAATTACCAAATGATGTTATTGAGTTAAATATGGAGGAAGCTTTTGGATTAGCTTTGCAGAAAGCTGTCCCTCTTGAAGCTATGGTTACTCCAAGATTAACTTTGGATGTTTAT---GCACCTTAATAT- Solanum_lycopersicum_SL2.40sc03876 ATGGCGTTACGTATTAAT---GAGTTATTT---GTTGCGGCTATAATATATATCATAGTACATATTATTATTTCAAAATTAATAACCACCGTCCGGGAGCGGGGGCGGCGACTACCGCTACCGCCGGGTCCGACGGGGTGGCCGGTGATCGGAGCACTACCACTTTTAGGTTCAATGCCACATGTTGCACTTGCAAAAATGGCCAAAAAATATGGACCTATTATGTATTTAAAAGTTGGTACATGTGGGATGGTTGTTGCTTCTACCCCTAATGCTGCTAAAGCTTTCTTGAAAACACTTGATATTAATTTCTCTAATCGTCCACCTAATGCAGGTGCCACACATTTGGCCTATAATGCCCAAGACATGGTTTTTGCACCCTATGGACCACGTTGGAAGTTGCTAAGAAAATTGAGCAACTTACACATGCTAGGTGGAAAAGCTTTAGAAAATTGGGCCAACGTTCGTGCCAATGAGCTAGGTCACATGCTAAAATCGATGTTCGATGCAAGCCAGGATGGCGAATGTGTGGTGATTGCTGATGTGTTAACGTTTGCGATGGCAAATATGATTGGTCAAGTAATGTTGAGTAAAAGAGTGTTTGTTGAAAAAGGGGTTGAGGTTAATGAATTTAAGAATATGGTTGTGGAATTAATGACGGTTGCAGGATATTTTAATATTGGTGATTTTATACCTAAGTTAGCTTGGATGGATATACAAGGAATTGAAAAAGGGATGAAAAATTTGCATAAAAAATTTGATGATTTATTGACAAAAATGTTTGATGAACATGAAGCAACTAGCAATGAAAGAAAAGAAAATCCTGATTTTCTTGATGTTGTTATGGCAAATAGGGATAATTCAGAAGGAGAAAGGCTAAGTACAACAAATATAAAAGCACTTTTGCTGAATTTATTCACTGCTGGTACAGACACTTCATCAAGTGTAATAGAATGGGCCCTTGCAGAAATGATGAAAAATCCTAAAATTTTCGAAAAAGCACAACAAGAAATGGACCAAGTAATTGGCAAAAACAGACGTTTAATTGAGTCTGATATTCCAAATCTTCCTTATTTACGTGCAATTTGCAAAGAAACATTTCGAAAACATCCCTCAACGCCACTAAATCTCCCTAGGGTATCGAGCGAGCCATGCACGGTCGATGGTTACTACATACCAAAAAATACTAGGCTTAGTGTCAACATATGGGCAATTGGACGAGATCCTGACGTGTGGGAGAATCCGCTCGAGTTCACTCCCGAGAGGTTCCTTAGCGGGAAAAACGCAAAGATTGAACCTCGTGGGAATGATTTCGAGTTAATTCCATTTGGTGCGGGACGAAGGATTTGCGCGGGGACAAGGATGGGAATAGTGATGGTGGAATATATATTGGGAACTTTGGTTCATTCATTTGATTGGAAATTACCAAATAATGTTATTGATATTAATATGGAGGAATCTTTTGGATTAGCTTTGCAAAAAGCTGTCCCTCTAGAAGCTATGGTTACTCCAAGGCTATCTTTGGACGTTTAT---CGTTGCTGATCG- Solanum_tuberosum_AY675558 atgacgttacgtatt---agtgagttgttt---gccgcggcaataatatacatcatagtacatattattatttcaaaattaatagccaccgtccgggagcgggggcggcgg------ctaccgccgggtccgacggggtggccggtgatcggagcactatcacttttaggttcaatgccacatgttgcacttgcaaaaatggccaaaaattatggacctattatgtatttaaaagttggtacatgtgggatggttgttgcctctacccctaatgctgcaaaagctttcttgaaaacacttgatattaatttttccaatcgtccacctaatgcaggtgccacacatttggcctataatgcccaagacatggtttttgcaccctatggacctcgttggaagttgctaaggaaattgagcaacttacagatgctaggtggaaaagccttagaaaattgggccaatgttcgtgccaatgagctaggtcacatgataaagtcgatgttcgatgcaagccacgtgggcgaatgtgtggtgattgctgatatgttgacgttcgcgatggcaaatatgattggtcaagtgatgttaagtaagagagtgttcgtggaaaaaggggcagaggttaatgaatttaagaatatggttgtggaattaatgacggttgcagggtattttaatattggtgattttattcctaaattagcttggatggatttacaaggaattgaaaaagggatgaaaagtttgcataaaaaatttgatgatttattgacaaaaatgtttgatgaacatgaagcaactacctatgaaagaaaagaaaatcctgattttcttgatgttgttatggcaaataaggataattctgaaggagaaaggcttagtacaacaaatatcaaagcacttttgctgaatttgttcacagctggtacagacacttcatctagtgtaatagaatgggcccttgcagaaatgatgaaaaatcctaaaattttcaaaaaagcacaagaagaaatggaccaagtaattggcaaaaatagacgtttaattgaatctgatattccaaatcttccttatttacgtgcaatttgcaaagaaacatttcggaaacatccttcaacaccactaaatctccctagagtatcgaccgagccgtgcacggtcgatggttactacataccgaaaaatactagactcagtgtcaacatatgggcaatcggacgagatcctgacgtgtgggagaatccacttgagttcaatcccgagaggttcctgagcgggaaaaacgcaaagattgaacctcgtgggaacgatttcgagttaattccatttggggcaggacgaaggatttgcgcggggacaaggatgggaatagtgatggtggaatatatattgggaactttggttcattcatttgattggaaattaccaaatgatgttattgatattaatatggaggaatcttttggattagctttgcaaaaagctgtccctcttgaagctatggttactccaaggctatctttggacgtttat---tgttgctgatcg- Iochroma_cyaneum_KJ094354 atggtgttactacttaatagtgagttgtgt---gcagcagctataatatttatcatagtacatattattatttcaaaattaatagccaccgcc------cgggggcagcgt------ctgcccccaggtccgatggggtggccggtggtcggagcacttccgcttttaggtgccatgccacatgttgcacttgcaaaaatggccaaaaaatatggacctattatgtatctcaaagttggaacatgtgggatggttgttgcttctactcctaatgctgctaaagctttcttgaaaatacttgatatcaatttctccaatcgtccacctaatgcaggtgccacacacttggcctataatgcccaagacatggtttttgcacactatggaccacgttggaagttgctaaggaaattgagcaacttacacatgctaggtggaaaagccttagaagattgggccaatgtccgcgccaatgagctaggccacatgctaaaatcaatgttcgacgcgagccgagagggcgagcgggttgtggtggcggatatgttgacgttcgcaatggcaaacatgattggccaagtgatattaagtaagagagtgttcgtggaaaaaggagcagaagtcaacgaatttaaggacatggttgtggaattgatgaccgtagcagggtattttactatcggcgattttattcctatattagcttggatggatttacaagggattgaaagaggcatgaaaagtttgcacaaaaagtttgatgatctattgacaaaaatgtttgaggaacataaagcaactagctatgaaagaaaggggaaacctgattttcttgattttgttatggcaaatagggacaattctgaaggagaaaggctcagtacaaccaatatcaaagcacttttgctgaatttgtttactgccggtacagacacttcatcaagtgcaatagaatgggcacttgcagaaatgatgaaaaatcctaaaattctcaaaaaagcacaacaagaaatggatcaaatcattggcaaaaacagacgttttattgaatctgacattccaaatctcccttatttacgtgcaatttgtaaagaagcatttcgaaaacatccttcaacaccattaaatctccctaggatatcgaacgagccgtgcacgatcgatggttactacataccaaaaaacaccaggctcagcgttaacatatgggcgattggacgagaccctgatgtgtgggagaatccactcgagttcaaccccgagaggttcctgagtgggaaaaacgcaaagattgaccctcgaggaaatgatttcgagttaattccatttggtgcaggacgaagaatttgtgcagggacaaggatgggaatagtgatggtggagtatatattgggaactttgattcattcatttgattggaaattaccaactgatgttattgatattaatatggatgaatcttttggattggctttgcaaaaggctatccctcttgaagctatggttactccaaggctacctttggatgtttattatgcaaattga---- Iochroma_calycinum_KJ094346 ATGGTGTTACTACTTAATAGTGAGTTGTGT---GCAGCAGCTATAATATTTATCATAGTACATATTATTATTTCAAACTTAATAGCCACCGTC------CGGGGGCAGCGT------CTGCCCCCAGGTCCGATGGGGTGGCCGGTGGTCGGAGCACTTCCCCTTTTAGGTGCCATGCCACATGTTGCACTTGCAAAAATGGCCAAAAAATATGGACCTATTATGTATCTCAAAGTTGGAACATGTGGGATGGTTGTTGCTTCTACTCCTAATGCTGCTAAAGCTTTCTTGAAAACACTTGATAGTAATTTCTCCAATCGTCCACCTAATGCAGGTGCCACACACTTGGCCTATAATGCCCAAGACATGGTTTTTGCACACTATGGACCACGTTGGAAGTTGCTAAGGAAATTGAGCAACTTACACATGCTAGGTGGAAAAGCCTTAGAAGATtGGGCCAATGTCCGCGCCAATGAGCTAGGCCACATGCTAAAATCAATGTTCGACGCCAGCCGAGAGGGCGAGCGGGTGGTGGTGGCGGATATGTTGACGTTCGCAATGGCAAACATGATTGGCCAAGTGGTATTAAGTAAGAGAGTGTTCGTGGAAAGAGGAGCAGAAGTCAACCAATTTAAGGACATGGTTGTGGAATTGATGACCGTAGCAGGGTATTTTAATATCGGAGATTTTATTCCTATATTAGCTTGGATGGATTTACAAGGGATTGAAAGAGGCATGAAAAGTTTGCACAAAAAGTTTGATGATCTATTGACAAAAATGTTTGAGGAACATAAAGCAACTAGCTATGAAAGAAAGGGGAAGCCTGATTTTCTTGATTTTGTTATGGCAAATAGGGACAATTCTGAAGGAGAAAGGCTCAGTACAACCAATATCAAAGCACTTTTGCTGAATTTGTTTACTGCCGGTACAGACACTTCATCAAGTGCAATAGAATGGGCACTTGCAGAAATGATGAAAAATCCTAAAATTCTCAAAAAAGCACAAGAAGAAATGGATCAAACCATTGGCAAAAACAGACGTTTAATTGAATCTGACATTCCAAATCTCCCTTATTTACGTGCAATTTGTAAAGAAGCATTTCGAAAACACCCTTCAACACCATTAAATCTCCCTAGGATATCGAACGAGCCATGCACAGTCGATGGTTACTACATACCAAAAAACACCAGGCTCAGTGTTAACATATGGGCGATTGGACGAGACCCTAATGTGTGGGAGAATCCACTCGAGTTCAACCCCGAGAGGTTCTTGAGTGGGAAAAATGCAAAGATTGACCCTCGAGGAAATGATTTCGAGTTGATTCCATTTGGTGCAGGACGAAGAATTTGTGCAGGGACAAGGATGGGAATAGTGATGGTGGAGTATATATTGGGAACTTTGGTTCATTCATTTGATTGGAAATTACCAAATGATGTAATTGATATTAATATGGAGGAGTCTTTTGGATTAGCTTTGCAAAAGGcTGTCCCTCTTGAAGCTATGGTTACTCCAAGGCTACCTTTGGATGTTTATTATGCAAATTGA---- Iochroma_calycinum_KJ094345 ATGGTGTTACTACTTAATAGTGAGTTGTGT---GCAGCAGCTATAATATTTATCATAGTACATATTATTATTTCAAACTTAATAGCCACCGTC------CGGGGGCAGCGT------CTGCCCCCAGGTCCGATGGGGTGGCCGGTGGTCGGAGCACTTcCCCTTTTAGGTGCCATGCCACATGTTGCACTTGCAAAAATGGCCAAAAAATATGGACCTATTATGTATCTCAAAGTTGGAACATGTGGGATGGTTGTTGCTTCTACTCCTAATGCTGCTAAAGCTTTCTTGAAAACACTTGATAGTAATTTCTCCAATCGTCCACCTAATGCAGGTGCCACACACTTGGCCTATAATGCCCAAGACATGGTTTTTGCACACTATGGACCACGTTGGAAGTTGCTAAGGAAATTGAGCAACTTACACATGCTAGGTGGAAAAGCCTTAGAAGATtGGGCCAATGTCCGCGCCAATGAGCTAGGCCACATGCTAAAATCAATGTTCGACGCCAGCCGAGAGGGCGAGCGGGTGGTGGTGGCGGATATGTTGACGTTCGCAATGGCAAACATGATTGGCCAAGTGGTATTAAGTAAGAGAGTGTTCGTGGAAAAAGGAGCAGAAGTCAACCAATTTAAAGACATGGTTGTGGAATTGATGACCGTAGCAGGGTATTTTAATATCGGAGATTTTATTCCTATATTAGCTTGGATGGATTTACAAGGGATTGAAAGAGGCATGAAAAGTTTGCACAAAAAGTTTGATGATCTATTGACAAAAATGTTTGAGGAACATAAAGCAACTAGCTATGAAAGAAAGGGGAAGCCTGATTTTCTTGATTTTGTTATGGCAAATAGGGACAATTCTGAAGGAGAAAGGCTCAGTACAACCAATATCAAAGCACTTTTGCTGAATTTGTTTACTGCCGGTACAGACACTTCATCAAGTGCAATAGAATGGGCACTTGCAGAAATGATGAAAAATCCTAAAATTCTCAAAAAAGCACAAGAAGAAATGGATCAAACCATTGGCAAAAACAGACGTTTAATTGAATCTGACATTCCAAATCTCCCTTATTTACGTGCAATTTGTAAAGAAGCATTTCGAAAACACCCTTCAACACCATTAAATCTCCCTAGGATATCGAACGAGCCATGCACAGTCGATGGTTACTACATACCAAAAAACACCAGGCTCAGTGTTAACATATGGGCGATTGGACGAGACCCTAATGTGTGGGAGAATCCACTCGAGTTCAACCCCGAGAGGTTCTTGAGTGGGAAAAATGCAAAGATTGACCCTCGAGGAAATGATTTCGAGTTGATTCCATTTGGTGCAGGACGAAGAATTTGTGCAGGGACAAGGATGGGAATAGTGATGGTGGAGTATATATTGGGAACTTTGGTTCATTCATTTGATTGGAAATTACCAAATGATGTAATTGATATTAATATGGAGGAGTCTTTTGGATTAGCTTTGCAAAAGGCTGTCCCTCTTGAAGCTATGGTTACTCCAAGGCTACCTTTGGATGTTTATTATGCAAATTGA---- ; END; BEGIN MacClade; Version 4.0 84; LastModified -826034848; FileSettings editor '0' '0' '1' '1'; Singles 000; Editor 0011100111011110010001001 '4' '8' Geneva '9' '208' '1' all; EditorPosition '58' '141' '691' '1759'; TreeWindowPosition '46' '6' '959' '1230'; ListWindow Characters closed Geneva '9' '50' '10' '273' '406' 000; ListWindow Taxa closed Geneva '9' '50' '10' '209' '490' 100000; 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' '942' '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 '779' '1035' '115' '165'; TreeToolsPosition '844' '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' '-17321' '-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' '0' 100000101110001; PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010; BothTools '1'; END; BEGIN TREES; Title F35h_ML_Tree; LINK Taxa = Taxa; TRANSLATE 1 Petunia_hybrida_D14588, 2 Nicotiana_benthamiana_V0.4.2.Scf45423, 3 Solanum_lycopersicum_SL2.40sc03876, 4 Solanum_tuberosum_AY675558, 5 Iochroma_cyaneum_KJ094354, 6 Iochroma_calycinum_KJ094346, 7 Iochroma_calycinum_KJ094345; TREE F35h_ML_Tree = (1:0.046479,(2:0.075515,((3:0.031956,4:0.020593):0.059751,(5:0.010626,(6:6.45E-4,7:6.51E-4):0.011074):0.030611):0.098965):0.046479)[% ] [% ] [% setBetweenBits = selected ]; END; BEGIN NOTES; TEXT TAXA = Taxa TAXON = 4 TEXT = 'AY675558.__Solanum_tuberosum_flavonoid_3'',5''-hydroxylase_(P)_mRNA,_complete'; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS; TYPESET * UNTITLED = unord: 1 - 1549; END; BEGIN CODONS; CODONPOSSET * UNTITLED = N: 1549, 1: 1 - 1546\3, 2: 2 - 1547\3, 3: 3 - 1548\3; CODONPOSSET CodonPositions = N: 1549, 1: 1 - 1546\3, 2: 2 - 1547\3, 3: 3 - 1548\3; CODESET * UNTITLED = universal: 1 - 1549; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1549; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1406497468037; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6812361265243622538; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 134222633497658125; mqVersion 275; checksumv 0 3 1250830212 null getNumChars 1549 numChars 1549 getNumTaxa 7 numTaxa 7 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 242913.0 sumSquares -2.0153067900527685E21 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 349; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 749 464; setLocation 39 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6812361265243622538 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6812361265243622538; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; getTable; tell It; rowNamesWidth 220; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 400 397; setLocation 39 22; 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.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 400 397; setLocation 39 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 #6812361265243622538 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1207.1406497370929.6728640270245839978; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 400 397; setLocation 39 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; 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; 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; endTell; end;