#NEXUS [written Tue Jul 19 22:10:05 CAT 2016 by Mesquite version 3.04 (build 725) at Bullseye/192.168.56.1] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=27; TAXLABELS 'Trichoderma neorufum GJS_96_132' 'Trichoderma neorufum GJS _96_135' Trichoderma_hamatum_DAOM167057 Trichoderma_hamatum_PPRI20673 'Trichoderma hamatum GJS_04_203' 'Trichoderma evansii Dis_380a' 'Trichoderma evansii DIS_341HI' 'Trichoderma flaviconidium GJS_99_49' 'Trichoderma pubescens DAOM_166162' 'Trichoderma pubescens DAOM_229987' 'Trichoderma pezizoides GJS01_257' Trichoderma_eijii_TUFC100002 Trichoderma_eijii_8139 'Trichoderma paucisporum GJS_01_13' 'Trichoderma paucisporum GJS_0369' 'Trichoderma theobromicola Dis_85f' 'Trichoderma theobromicola Dis_376f' 'Trichoderma lieckfeldtiae GJS04_196' 'Trichoderma lieckfeldtiae GJS_0501' 'Trichoderma asperelloides GJS_99_6' Trichoderma_asperelloides_PPRI20679 'Trichoderma asperelloides GJS_04_116' 'Trichoderma asperellum GJS_01_294' 'Trichoderma asperellum GJS_91_162' Trichoderma_asperellum_PPRI20669 'Trichoderma yunnanense CBS _21219' 'Trichoderma strigosum DAOM_166121' ; END; BEGIN CHARACTERS; TITLE 'Matrix in file "ML tree of hamatum known spp amb removed.nex"'; DIMENSIONS NCHAR=344; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Trichoderma neorufum GJS_96_132' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGTTTCATTTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCATCG--CAACACAATTTGT---CTCCATTGCACCGTCAAATGCTTTGTGATTCATTGTGCTGACCAGGTATTCAATTATAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCTGTTCTTCTCAGACCGCGTCTGAAGATGGCCATTCTAAC 'Trichoderma neorufum GJS _96_135' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGTTTCATTTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCATCG--CAACACAATTTGTCTCCTCCATTGCACCGTCAAATGCTTTGTGATTCATTGGGCTGACCAGGTATTCAATTATAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCTGTTCTTCTCAGACCGCGTCTGAAGATGGCCATTCTAAC Trichoderma_hamatum_DAOM167057 TCTGGCTGCCTTGGTTGGTTTTTAGTGGGGTGCCAAATTTGGCAGTGACCCCGCCATCGCCACTGTTCCTCATGCACTACCCAACACATGCTACGT----------------ATCAACTGCTTGGTTCATTGTGCTAATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TGGTCACTATCCCAACATCATCATGCTAAC Trichoderma_hamatum_PPRI20673 TCTGGCTGCCTTGGTTGGTTTTTAGTGGGGTGCCAAATTTGGCAGTGACCCCGCCATCGCCACTGTCCCTCACGCATTACCCAACACAAGCTACTT----------------ATCAACTGCTTGGTTCATTGTGCTAATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TGTTCACTATCCCAACATCATCATGCTAAC 'Trichoderma hamatum GJS_04_203' TCTGGCTGCCTTGGTTGGTTTTTAGTGGGGTGCCAAATTTGGCAGTGACCCCGCCATCGCCACTGTCCCTCATGCAGTACCCAACATATTCTACA-----------------GTCAACGTCTTGGTTCATTGTGCTAATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TGTTCACTATCCCAACATCATCATGCTAAC 'Trichoderma evansii Dis_380a' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGTCACTGTCCCT---CCATCACCCGACACATTCTACTTGTCAATT---------AATTTGATTTTGGTTCATTGTACTAATCATCTTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TAGTCGATATTTCAAGACCATCATTCTAAC 'Trichoderma evansii DIS_341HI' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGTCACTGTCCCT---CCATCACCCGACACATTCTACTTGTCAATT---------AATTTGATTTTGGTTCATTGTACTAATCATCTTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TAGTCGATATTTCAAGACCATCATTCTAAC 'Trichoderma flaviconidium GJS_99_49' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGG-GCCAATTTTGGCAGCAACCCCGCTATCGCCACTGGCCCTCGTCCATCGCCCAACACACTCTCGAG----------------TTGCTCTTTTGGGTTCATGGTGCTAATCATACTTCGATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTTGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCGAC-TAGTCGATATTCCAACATCATCTCGCTAAC 'Trichoderma pubescens DAOM_166162' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGCCAAATTTGGCAGCAACCCCGCTATTGCCACTGT--CTCACACATTGCCCAACATATTTTACTTCAATC-----------AATTTCTGTTTGGTTCATTGTACTAATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTTCGACTTCGGTAATA-TCCAACATCATCATTCTAAC 'Trichoderma pubescens DAOM_229987' TCTGGCTGCCTTGTTTGGTTTTTAGTGGGGTGCCAAATTTGGCAGCAACCCCGCTATTGCCACTGT--CTCACACATTGCCCAACATATTTTACTTCAATC-----------AATTTCTGTTTGGTTCATTGTACTAATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTATTATGTCACCGTCATTGGTATGTTTTCAGTTCGACTTCGGTAATATTCCAACATCATCATTCTAAC 'Trichoderma pezizoides GJS01_257' TCTTGCTGCCTTGTTTGGTTTTTAGTGGGGTATCAAGTTTGGCAGCAACCCCGCTATCGCCACTGCCCCTCGTCCATCGCCCAACACACTCTACTTCGAATCT---------TTGATTTTTGTAATTCATTTTATTAATCATACTCGACTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTAGCCC-TCGTCGATACCTCG---CCATCATTCTAAC Trichoderma_eijii_TUFC100002 TCTTGCTGCCTTGTTTGGTTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGCCGCTGCCCCTCGTCCATCGCCCAACACACTCAACTTCAAATCTC--------TAGAGTTATTTAATTCATTTTATTAATCATACTCGACTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCCAC-TCGTCGATACTTCAAGGCCATCAT?????? Trichoderma_eijii_8139 TCTTGCTGCCTTGTTTGGTTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGCCGCTGCCCCTCGTCCATCGCCCAACACACTCAACTTCAAATCTC--------TAGAGTTATTTAATTCATTTTATTAATCATACTCGACTCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCAGTCCCAC-TCGTCGATACTTCAAGGCCATCATTCTAAC 'Trichoderma paucisporum GJS_01_13' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTCTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCACTGCCCAACACATTTTACCTGCTCAGTCGTATCGTCAATTTCTCTTCGGTTCATTGTGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCGGTCATCGTTACTTGACATGTCAAGATCATCATTCTAAC 'Trichoderma paucisporum GJS_0369' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTCTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCACTGCCCAACACATTTTACCTGCTCAGTCGTATCGTCAATTTCTCTTCGGTTCATTGTGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCGGTCATCGTTACTTGACATGTCAAGATCATCATTCTAAC 'Trichoderma theobromicola Dis_85f' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTAATTTTTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCACTGCCCAACAGATTTTACTTGCTCAGTCGTATCGTCAATTTCTTTTCGGTTCATTGTGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAGGTTTTCAGTCCTCGTTACTTGACATGTCAAAATCATCAATCTAAC 'Trichoderma theobromicola Dis_376f' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCATTTTTGGCAGCAACCCCGCTATCGCCACTGTCCCTCATCCACTGCCCAACAGATTTTACTTGCTCAGTCGTATCGTCAATTTCTTTTCGGTTCATTGTGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAGGTTTTCAGTCCTCGTTACTTGACATGTCAAAATCATCAATCTAAC 'Trichoderma lieckfeldtiae GJS04_196' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATGTTGGCAGCAACCCCGCTATTGCCACCGTCGCT---CCATCGCCCAGCATATTCCACTTGCTCAATCGCATCGTCAATTTCTTTTCGGTTCATTGTGCTGATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTGCGGTCCTACTTGGTCGATATTTCGAGATTGTCATTCTAAC 'Trichoderma lieckfeldtiae GJS_0501' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATGTTGGCAGCAACCCCGCTATTGCCACCGTCGCT---CCATCGCCCAGCATATTCCACTTGCTCAATCGCATCGTCAATTTCTTTTCGGTTCATTGTGCTGATCATACTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTGCGGTCCTACTTGGTCGATATTTCGAGATTGTCATTCTAAC 'Trichoderma asperelloides GJS_99_6' TCTCGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTTTGACGGCAACCCCACTATCGCCACTGTACCTCTTCCATCATCCACCACATGCT-TTTGTTCAATCGCATCGTCA---TATCTCTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACACTT--CAGTCGACATTGCAAGATCGTCATTCTAAC Trichoderma_asperelloides_PPRI20679 TCTCGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTTTGACGGCAACCCCACTATCGCCACTGTACCTCTTCCATCATCCACCACATGCT-TTTGTTCAATCGCATCGTCA---TATCTCTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACACTT--CAGTCGACATTGCAAGATCGTCATTCTAAC 'Trichoderma asperelloides GJS_04_116' TCTCGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTTTGACGGCAACCCCACTATCGCCACTGTACCTCTTCCATCATCCACCACATGCTATTTGTTCAATCGCATCGTCA---TATCTCTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACACTT--CAGTCGACATTGCAAGATCGTCATTCTAAC 'Trichoderma asperellum GJS_01_294' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGCCACTGCACCTCTTCCATCACCCACCACATGCTATTTGCTCAATCGCGTCGTC-----TTTTTTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACTCTTCTCTATCGACATTCCAAGTCCGCCATTCTAAC 'Trichoderma asperellum GJS_91_162' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGCCACTGCACCTCTTCCATCACCCACCACATGCTATTTGCTCAATCGCGTCGTC-----TTTTTTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACTCTTCTCTATCGACATTCCAAGTCCGCCATTCTAAC Trichoderma_asperellum_PPRI20669 TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAAATTTGGCAGCAACCCCGCTATCGCCACTGCACCTCTTCCATCACCCACCACATGCTATTTGCTCAATCGCGTCGTC-----TTTTTTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTGGACTCTTCTCTATCGACATTCCAAGTCCGCCATTCTAAC 'Trichoderma yunnanense CBS _21219' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGTCAATTTTGGCAGCAACCCCGCTATCGCCACTGCACCTCTTCTATCACCCACCACATGCTATTTGCTCAATCGCATCGTCATCTCTATTTTTGTTCATTATGCTGATCATGCTTCAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTAGGCTCTTCTCAGTCGACATCGCAAGTCCGCCATTCTAAC 'Trichoderma strigosum DAOM_166121' TCTGGCTGCCTTGTTTGGCTTTTAGTGGGGTGCCAGCTTGGCAAGCAACCCCGCTATCGCCACTGTAGCTCGTCCATCGCCCAACACATTCTACTC-TACCATCGCATCGTCCGAAATCTCTTGATTCATTATGCTGATCATCTTTCAATCAATAGGAAGCCGCCGAACTCGGAAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTTAGTTTCC--TCATTGACATCTCGAAATCATCATTCTAAC ; END; BEGIN TREES; Title 'Trees from "ML tree of hamatum known spp amb removed.nex"'; LINK Taxa = Taxa; TRANSLATE [0] 1 'Trichoderma neorufum GJS_96_132', [1] 2 'Trichoderma neorufum GJS _96_135', [2] 3 Trichoderma_hamatum_DAOM167057, [3] 4 Trichoderma_hamatum_PPRI20673, [4] 5 'Trichoderma hamatum GJS_04_203', [5] 6 'Trichoderma evansii Dis_380a', [6] 7 'Trichoderma evansii DIS_341HI', [7] 8 'Trichoderma flaviconidium GJS_99_49', [8] 9 'Trichoderma pubescens DAOM_166162', [9] 10 'Trichoderma pubescens DAOM_229987', [10] 11 'Trichoderma pezizoides GJS01_257', [11] 12 Trichoderma_eijii_TUFC100002, [12] 13 Trichoderma_eijii_8139, [13] 14 'Trichoderma paucisporum GJS_01_13', [14] 15 'Trichoderma paucisporum GJS_0369', [15] 16 'Trichoderma theobromicola Dis_85f', [16] 17 'Trichoderma theobromicola Dis_376f', [17] 18 'Trichoderma lieckfeldtiae GJS04_196', [18] 19 'Trichoderma lieckfeldtiae GJS_0501', [19] 20 'Trichoderma asperelloides GJS_99_6', [20] 21 Trichoderma_asperelloides_PPRI20679, [21] 22 'Trichoderma asperelloides GJS_04_116', [22] 23 'Trichoderma asperellum GJS_01_294', [23] 24 'Trichoderma asperellum GJS_91_162', [24] 25 Trichoderma_asperellum_PPRI20669, [25] 26 'Trichoderma yunnanense CBS _21219', [26] 27 'Trichoderma strigosum DAOM_166121'; TREE tree_1 = ((((((((((3:0.023722,4:0.016255):0.00871,5:0.039725):0.120409,(9:0.0,10:0.006118):0.083177):0.032986,8:0.148652):0.027833,(6:0.0,7:0.0):0.070607):0.009389,((12:0.0,13:0.0):0.024704,11:0.06997):0.185441):0.060048,(18:0.0,19:0.0):0.0865):0.016436,(((((23:0.0,24:0.0):0.0,25:0.0):0.03585,26:0.033297):0.03138,((20:0.0,22:0.0):0.0,21:0.0):0.071725):0.109827,(1:0.0,2:0.006139):0.312811):0.014484):0.004353,((16:0.005837,17:0.0):0.036007,(14:0.0,15:0.0):0.025515):0.066803):0.144022,27:0.144022); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of hamatum known spp amb removed.nex"') = unord: 1 - 344; END; BEGIN NOTES; ALTTAXNAMES * UNTITLED = AF348115_H_neorufa_strain_GJS_96_132 AF487670_H_neorufa_T_strain_G_J_S__96_135 AF456911_T_hamatum_T_strain_DAOM_167057 EF_Tri_78 EU883565_T_hamatum_strain_GJS_04_203 EU856320_T_evansii_strain_Dis_380a EU883566_T_evansii_T_strain_DIS_341HI DQ020001_H_flaviconidia_T_gjs_99_49 AY750887_T_pubescens_T_Daom_166162 Trichoderma_pubescens___EU279964 AY937438_H_pezizoides_T_strain_GJS_01_257 JX684011_T_eijii_T_strain_TUFC_100002 Trichoderma_eijii_8139___KJ634769 DQ109540_T_paucisporum_T_strain_GJS_01_13 DQ109541_T_paucisporum_strain_GJS_03_69 EU856321_T_theobromicola_T_strain_Dis_85f EU856322_T_theobromicola_strain_Dis_376f EU856324_T_lieckfeldtiae_strain_GJS_04_196 EU856328_T_lieckfeldtiae_strain_GJS_05_01 DQ109550_T_asperelloides_strain_GJS_99_6 EF_Tri_150 GU248412_T_asperelloides_T_strain_GJS_04_116 'EU856323_T_asperellum_T_strain_GJS_01_294__cbs443.97_' Trichoderma_asperellum_gjs_91_162___FJ463285 EF_Tri_10 GU198243_T_yunnanense_T_strain_CBS_121219 Trichoderma_strigosum_OUT___AY937442__modified_; ALTTAXNAMES Alternative_Naming2 = 'Trichoderma neorufum GJS_96_132' 'Trichoderma neorufum GJS _96_135' Trichoderma_hamatum_DAOM167057 Trichoderma_hamatum_PPRI20673 'Trichoderma hamatum GJS_04_203' 'Trichoderma evansii Dis_380a' 'Trichoderma evansii DIS_341HI' 'Trichoderma flaviconidium GJS_99_49' 'Trichoderma pubescens DAOM_166162' 'Trichoderma pubescens DAOM_229987' 'Trichoderma pezizoides GJS01_257' Trichoderma_eijii_TUFC100002 Trichoderma_eijii_8139 'Trichoderma paucisporum GJS_01_13' 'Trichoderma paucisporum GJS_0369' 'Trichoderma theobromicola Dis_85f' 'Trichoderma theobromicola Dis_376f' 'Trichoderma lieckfeldtiae GJS04_196' 'Trichoderma lieckfeldtiae GJS_0501' 'Trichoderma asperelloides GJS_99_6' Trichoderma_asperelloides_PPRI20679 'Trichoderma asperelloides GJS_04_116' 'Trichoderma asperellum GJS_01_294' 'Trichoderma asperellum GJS_91_162' Trichoderma_asperellum_PPRI20669 'Trichoderma yunnanense CBS _21219' 'Trichoderma strigosum DAOM_166121'; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of hamatum known spp amb removed.nex"') = universal: 1 - 344; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = 'Matrix in file "ML tree of hamatum known spp amb removed.nex"') = 'Jukes-Cantor': 1 - 344; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1468959005351; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6632064161664787369; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4547387063434532103; mqVersion 304; checksumv 0 3 1656507941 null getNumChars 344 numChars 344 getNumTaxa 27 numTaxa 27 short true bits 15 states 15 sumSquaresStatesOnly 218432.0 sumSquares 218432.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 340; 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 #6632064161664787369 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6632064161664787369; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; newAssistant #mesquite.lists.TaxonListArchivedName.TaxonListArchivedName; getTable; tell It; columnWidth 1 311; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1576 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 1576 889; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6632064161664787369 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 948.1468956533407.3677894246994650119; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1576 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 #4547387063434532103 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 226; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1576 889; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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;