#NEXUS [written Mon Jul 11 21:07:20 CAT 2016 by Mesquite version 3.04 (build 725) at Bullseye/192.168.56.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=23; TAXLABELS 'Trichoderma virens PPRI_20676' 'Trichoderma virens GJS_06_114' 'Trichoderma virens GJS_95-78' 'Trichoderma virens GLI_39' 'Trichoderma crassum DAOM_164916' 'Trichoderma virens DAOM_237548' 'Trichoderma helicum DAOM_230017' 'Trichoderma helicum DAOM_230016' 'Trichoderma spirale PPRI_20681' 'Trichoderma spirale DAOM_229883' 'Trichoderma spirale CBS_120963' 'Trichoderma spirale DAOM_183974' 'Trichoderma spirale DAOM_177714' 'Trichoderma longipile GJS_91-93' 'Trichoderma longipile DAOM_177227' 'Trichoderma longipile CBS_120953' 'Trichoderma fertile DAOM_167161' 'Trichoderma strictipile DAOM_167072' 'Trichoderma strictipile DAOM_172827' 'Trichoderma phyllostachydis CBS_114071' 'Trichoderma phyllostachydis GJS_92-123' 'Trichoderma gelatinosum GJS_88-17' 'Trichoderma gelatinosum CPK_1618' ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "ML tree of T. virens clade.nex"'; DIMENSIONS NCHAR=371; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Trichoderma virens PPRI_20676' AGT-GGGGGTGCACCAGCA----ACCCCACCACTACCT--CGCTGC-TCTTTGCCCTTGT-CTATCACTTCCCAGTCCTCATTC--AACA-ATCTGTGCCTCGTTA--GCTGCAGCGATGCTAACCACCATTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCGTCC----CATTCATCCAGCTCCCGCAAGCCAGTGCTAACCAGGACCT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma virens GJS_06_114' AGT-GGGGGTGCACCAGCA----ACCCCGCCACTACCT--CGCTGC-TCTTTGCCCTCGT-CTACCACTTCCTAGTCCTCATTC--AACG-ATCTGTGTCTCGTTA--TTTGCAGCGATGCTAACCACCGTCCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCGTCC----CATTCATCCAGCTCCCGCAAACCAGTGCTAACCAGGACCT--CACAGACGCCCCCGGCCACCGTGACTTCATC 'Trichoderma virens GJS_95-78' AGT-GGGGGTGCACCAGCA----ACCCCACCACTACCT--CGCTGC-TCTTTGCCATCGT-CTACCACTTCCCAGTCCTCATTC--AACG-ATCTGTGTCTCGTTA--TTTGCAGCGATGCTAACCACCGTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCGTCC----CATTCATCCAGCCCCCGCAAACCAGTGCTAACCAGGACCT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma virens GLI_39' AGT-GGGGGTGCACCAGCA----ACCCCACCACTACCT--CGCTGC-TCTTTGCCATCGT-CTACCACTTCCCAGTCCTCATTC--AACG-ATCTGTGTCTCGTTA--TTTGCAGCGATGCTAACCACCGTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCGTCC----CATTCATCCAGCCCCCGCAAACCAGTGCTAACCAGGACCT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma crassum DAOM_164916' AGT-GGGGGTGCGCCAGCA----ACCCCACCACTACCT--CGCTGC-TTTTTGCCCTCGT-CTACCACTTCCCAGTCCTCATTC--AACG-ATCTGTGTCTCGTTA--GTTGCAGCAATGCTAACCACCGTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCCGATACTATGTCACCGTCATTGGTATGTCTCATCA----CATTCATCCCGCAACTACAAACCAGTGCTAACCAAAACCT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma virens DAOM_237548' AGT-GGGGGTGCACCAGCA----ACCCCACCACTACCT--CGCTGC-TCTTTGCCCTTGTCCTATCACCTCCCAGTCCTCGTCC--AACG-ATCTGTGTCTCGATA--ATTGCAGCGATGCTAACCACCGTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCATCAC---TTTTCATCCAGCTCCCGCAAACCAGTGCTAACCAGGACCT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma helicum DAOM_230017' AGT-GGGGGCGCACAAGCA----ACCCCACCACTATCT--CGAAGC-TTTTTTTCCCTGCTCTATCAAT---------------------------TGTATCAATA---GTTCAGCGATGCTAACCACCTTTCCCTCTACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCATTCATCGCATCCGAGTCGCATCAGTCAGCCAGTGCTAACAATAGCTT--CACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma helicum DAOM_230016' AGT-GGGGGCGCACAAGCA----ACCCCACCACTATCT--CGTAGC-TTTTTTTCCCTGCTCTATCAAT---------------------------TGTATCAATA---GTTCAGCGATGCTAACCACCTTTCCCTCTACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCATTCATCGCATCCGAGTCGCATCAGTCAGCCAGTGCTAACAATAGCTT--CACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma spirale PPRI_20681' AGT-GGGGTTGCTGGTGC-----ACCCCACTGCTGCCTGTCACTGC-TTTTTGTCCTTCA-CTACGACCACCT------------------------------TCA--TTTTCAACGATGCTAACCATCTTTCCCTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGATATCGCTCTGTGGAAGTTCGAGACTCCTAAGTACTATGTCACCGTCATTGGTATGTTTGACTCATTACCTTCATGCTATAATTGCAACTCGGTGCTAACGCAAACAT--TACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma spirale DAOM_229883' AGT-GGGGTTGCTGGTGC-----ACCCCACTGCTGCCTGTCACTGC-TTTTTGTCCTTCA-CTACGACCACCT------------------------------TCA--TTTTCAACGATGCTAACCATCTTTCCCTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGATATCGCTCTGTGGAAGTTCGAGACTCCTAAGTACTATGTCACCGTCATTGGTATGTTTGACTCATTACCTTCATGCTATAATTGCAACTCGGTGCTAACGCAAACAT--TACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma spirale CBS_120963' AGT-GGGGTTGCTGGTGC-----ACCCCACTGCTGCCTGTCACTGC-TTTTTGTCCTTCA-CTACGACCACCT------------------------------TCA--TTTTCAACGATGCTAACCATCTTTCCCTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGATATCGCTCTGTGGAAGTTCGAGACTCCTAAGTACTATGTCACCGTCATTGGTATGTTTGACTCATTACCTTCATGCTATAATTGCAACTCGGTGCTAACGCAAACAT--TACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma spirale DAOM_183974' AGT--GGGGTGCACCAGCA----ACCCCACCGCCGCCTATCGCTGC-TTTTTGCCCTTCA-CTACGACTACACAGTTAC------------------------TCA--TTTTCAACGATGCTAACCATCTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGATATCGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCATTTATTACCTCCATGCTACAATTGCAACTCGGTGCTAATGCAAACAT--TACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma spirale DAOM_177714' AGTGGGGGTTGCACCAGCA----ACCCCACCGCTGCCTATCACTGCTTTTTTGTCCTTCA-CTACGACGACACAGTTAT------------------------TCA--TTTTCAGCGATGCTAATCATCTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTGTGGAAGTTCGAGACTCCTAAGTACTATGTCACCGTCATTGGTATGTCTGATTCACTACTTCCATGCTGCAATTGCAACTCGGTGCTAACGCAAACAT--CACAGACGCCCCCGGCCACCGTGATTTCATC 'Trichoderma longipile GJS_91-93' AGT-GGGGGCGCA-CAGCA----ACCCCACCACTGCCATTCACTGC-TTTTTGCACTTCA-CTACAACTCC-CAGCTGCCACTC--AGCACCTCTATATCTCGTCA--CTTTCAGCGATGCTAACCATCTTTCCCCCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCATTTCTGTGCTGTGTCTGCAAGCTTGTGCTAATGCAAACAT--GACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma longipile DAOM_177227' AGT-GGGGGCGCA-CAGCA----ACCCCACCACTGCCATTCACTGG-TTTTTGCACTTCA-CTACAACTCC-CAGCTGCCACTC--AGCACCTCTATATCTCGTCA--CTTTCAGCGATGCTAACCATCTTTCCCCCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCATTTCTGTGCTGCGTCTGCAAGCTTGTGCTAATGCAAACAT--GACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma longipile CBS_120953' AGT-GGGGGCGCA-CAGCA----ACCCCACCACTGCCATTCACTGG-TTTTTGCACTTCA-CTACAACTCC-CAGCTGCCACTC--AGCACCTCTATATCTCGTCA--CTTTCAGCGATGCTAACCATCTTTCCCCCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCATTTCTGTGCTGCGTCTGCAAGCTTGTGCTAATGCAAACAT--GACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma fertile DAOM_167161' AGT--GGGGTGTACCGGCA----ACCCCACTGCCGCTCACT------GTTCTGCCCTTGA-TTACCACTGCCCAG-TGTCATTC--AACGCTTTTGTGCCT-GTCA--CTTGCAGCGATGCTAACCACGTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATCGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCACATTCATGCGGCATCGGCAAGCATGTGCTAACACAAACTT--GACAGACGCTCCCGGCCATCGTGATTTCATC 'Trichoderma strictipile DAOM_167072' AGT--GGGGTGTACCAGCA----ACCCCACTGTCGCTCACT------GTTCTGCCCTTCA-TTCCCACTACCCAG-TGTCATTC--AACGCTTTTGTGCCT-GTCA--CTTGCAGCGATGCTAACCATGTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATCGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCACATTCATGCGGCATCGGCAAGCATGTGCTAACACAAACTT--GACAGACGCTCCCGGCCATCGTGATTTCATC 'Trichoderma strictipile DAOM_172827' AGT--GGGGTGTACCAGCA----ACCCCACTGCCGCTCACT------GTTCTGCCCTTCA-TTCCCACTACCCAG-TGTCATTC--AACGCTTTGGTGCCT-GTCA--CTTGCAGCGATGCTAACCATGTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTACGCATGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATCGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGATTCATCACATTCATGCGGCATCGGCAAGCATGTGCTAACACAAACTT--GACAGACGCTCCCGGCCATCGTGATTTCATC 'Trichoderma phyllostachydis CBS_114071' AGT-GGGGGCGCACCGGCA----ACCCCACCACTGCCA---------CTTTTGCCCTTCA-CTGCCGTTATCCAGTTACCATTTCAAACGCTTTTGTGTGTCATCACTTTCACAGCGATGCTAACCATTTTTCCCTCGATAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGCATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCTCAACTACGTGGTCACCGTCATTGGTATGTCTGATCCATCACCTCGATGCGGCATTCGCAAGCCTATGCTAACGCAAACTT--GACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma phyllostachydis GJS_92-123' AGT-GGGGGCGCACCGGCA----ACCCCACCACTGCCA---------CTTTTGCCCTTCA-CTGCCGTTATCCAGTTACCATTTCAAACGCTTTTGTGTGTCATCACTTTCACAGCGATGCTAACCATTTTTCCCTCGATAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGCATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCTCAACTACGTGGTCACCGTCATTGGTATGTCTGATCCATCACCTCGATGCGGCATTCGCAAGCCTATGCTAACGCAAACTT--GACAGACGCTCCCGGCCACCGTGATTTCATC 'Trichoderma gelatinosum GJS_88-17' AGT-GGGGTGGCACCAGCATTCCCCCCCACCACCACCTCTCACTGC-TTTCTGCTCTTGT-CTACCGCTACACTGTTGCCATTC--AGCGCTTTTGCGTCTCGT----------GCGATGCTAACCGCCTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACTGTCATTGGTATGTCTGATCTATGA---CCGTCCTCCGACAGCTAGCCCGTGCTAATCGAAGTCTCACACAGATGCTCCCGGCCATCGTGATTTCATC 'Trichoderma gelatinosum CPK_1618' AGT-GGGGTGGCACCAGCATTCCCCCCCACCACCACCTCTCACTGC-TTTCTGCTCTTGT-CTACCGCTACACTGTTGCCATTC--AGCGCTTTTGTGTCTCGT----------GCGATGCTAACCGCCTTTCCCTCAACAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACTGTCATTGGTATGTCTGATCTATGA---CCGTCCTCCGACAGCTAGCCCGTGCTAATCGAAGTCTCACACAGATGCTCCCGGCCATCGTGATTTCATC ; END; BEGIN TREES; Title 'Trees from "ML tree of T. virens clade.nex"'; LINK Taxa = Taxa; TRANSLATE [0] 1 'Trichoderma virens PPRI_20676', [1] 2 'Trichoderma virens GJS_06_114', [2] 3 'Trichoderma virens GJS_95-78', [3] 4 'Trichoderma virens GLI_39', [4] 5 'Trichoderma crassum DAOM_164916', [5] 6 'Trichoderma virens DAOM_237548', [6] 7 'Trichoderma helicum DAOM_230017', [7] 8 'Trichoderma helicum DAOM_230016', [8] 9 'Trichoderma spirale PPRI_20681', [9] 10 'Trichoderma spirale DAOM_229883', [10] 11 'Trichoderma spirale CBS_120963', [11] 12 'Trichoderma spirale DAOM_183974', [12] 13 'Trichoderma spirale DAOM_177714', [13] 14 'Trichoderma longipile GJS_91-93', [14] 15 'Trichoderma longipile DAOM_177227', [15] 16 'Trichoderma longipile CBS_120953', [16] 17 'Trichoderma fertile DAOM_167161', [17] 18 'Trichoderma strictipile DAOM_167072', [18] 19 'Trichoderma strictipile DAOM_172827', [19] 20 'Trichoderma phyllostachydis CBS_114071', [20] 21 'Trichoderma phyllostachydis GJS_92-123', [21] 22 'Trichoderma gelatinosum GJS_88-17', [22] 23 'Trichoderma gelatinosum CPK_1618'; TREE ML_tree = (20:0.0,21:0.0,((((7:0.006037,8:0.0):0.22248,((22:0.005443,23:0.0):0.196219,(5:0.062047,((1:0.032477,6:0.052705):0.015508,((3:0.0,4:0.0):0.011203,2:0.022613):0.000004):0.044173):0.096627):0.030254):0.063065,(17:0.021467,(18:0.005413,19:0.005514):0.006347):0.158012):0.009075,((14:0.004706,(15:0.0,16:0.0):0.005991):0.141148,(12:0.038971,(13:0.041946,(9:0.0,(10:0.0,11:0.0):0.0):0.101682):0.023782):0.103946):0.026998):0.197439); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of T. virens clade.nex"') = unord: 1 - 371; END; BEGIN NOTES; ALTTAXNAMES * UNTITLED = EF_Tri_101 Trichoderma_virens___FJ463364 Trichoderma_virens___FJ463366 Trichoderma_virens_T___GU591800 Trichoderma_crassum___EU280048 Trichoderma_virens___EU280065 Trichoderma_helicum___AY937433 Trichoderma_helicum___EU280055 EF_Tri_160 Trichoderma_spirale___EU280050 Trichoderma_spirale___FJ463291 Trichoderma_spirale_T___EU280049 Trichoderma_spirale___AY750896 Trichoderma_longipile___AY737727 Trichoderma_longipile___AY937430 Trichoderma_longipile_T___FJ860643 Trichoderma_fertile_T___AY750881 Trichoderma_strictipile___AY937450 Trichoderma_strictipile_T___AY937451 Trichoderma_phyllostachydis___FJ860673 Trichoderma_phyllostachydis_T___AY737745 Trichoderma_gelatinosum___AY737740 Trichoderma_gelatinosum___FJ179569; ALTTAXNAMES Alternative_Naming2 = 'Trichoderma virens PPRI_20676' 'Trichoderma virens GJS_06_114' 'Trichoderma virens GJS_95-78' 'Trichoderma virens GLI_39' 'Trichoderma crassum DAOM_164916' 'Trichoderma virens DAOM_237548' 'Trichoderma helicum DAOM_230017' 'Trichoderma helicum DAOM_230016' 'Trichoderma spirale PPRI_20681' 'Trichoderma spirale DAOM_229883' 'Trichoderma spirale CBS_120963' 'Trichoderma spirale DAOM_183974' 'Trichoderma spirale DAOM_177714' 'Trichoderma longipile GJS_91-93' 'Trichoderma longipile DAOM_177227' 'Trichoderma longipile CBS_120953' 'Trichoderma fertile DAOM_167161' 'Trichoderma strictipile DAOM_167072' 'Trichoderma strictipile DAOM_172827' 'Trichoderma phyllostachydis CBS_114071' 'Trichoderma phyllostachydis GJS_92-123' 'Trichoderma gelatinosum GJS_88-17' 'Trichoderma gelatinosum CPK_1618'; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of T. virens clade.nex"') = universal: 1 - 371; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of T. virens clade.nex"') = 'Jukes-Cantor': 1 - 371; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1468264040755; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 4856834121679511041; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8550703084908273185; mqVersion 304; checksumv 0 3 402113214 null getNumChars 371 numChars 371 getNumTaxa 23 numTaxa 23 short true bits 15 states 15 sumSquaresStatesOnly 168882.0 sumSquares 168882.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 258; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1916 961; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #4856834121679511041 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #4856834121679511041; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; newAssistant #mesquite.lists.TaxonListArchivedName.TaxonListArchivedName; getTable; tell It; columnWidth 1 283; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1658 889; setLocation -8 -8; 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 1658 889; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #4856834121679511041 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 1475.1468263824349.517656150679857539; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1658 889; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientRight; 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 off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; togglePrintName on; 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 off; 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 #8550703084908273185 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 412; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1658 889; setLocation -8 -8; 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; toggleShowPaleExcluded 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;