#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 21, 2025; 6:26 GMT TreeBASE (cc) 1994-2008 Study reference: Samuels G., Dodd S., Gams W., Castlebury L., & Petrini O. 2002. Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus. Mycologia, 94(1): 146-170. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S779] [ The following blocks are input data for analysis step 1237 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1237; DIMENSIONS NTAX=30; TAXLABELS Hypocrea_rufa_GJS99.105 Hypocrea_rufa_GJS99.140 Hypocrea_rufa_GJS99.203 Hypocrea_sp._GJS96.132 Hypocrea_vinosa_GJS99.83 Trichoderma_aggressivum_TH2_CBS100525 Trichoderma_aggressivum_TH2_CBS100526 Trichoderma_aggressivum_TH2_CBS433.95 Trichoderma_aggressivum_TH2_CBS689.94 Trichoderma_aggressivum_TH4_DAOM222156 Trichoderma_aggressivum_TH4_GJS99.29 Trichoderma_aggressivum_TH4_GJS99.30 Trichoderma_atroviride_GJS90.134 Trichoderma_atroviride_GJS95.10 Trichoderma_atroviride_GJS95.108 Trichoderma_harzianum_CBS226.95 Trichoderma_harzianum_CBS227.95 Trichoderma_harzianum_CBS273.78 Trichoderma_harzianum_GJS95.81 Trichoderma_harzianum_GJS99.225 Trichoderma_harzianum_GJS99.227 Trichoderma_harzianum_GJS99.230 Trichoderma_harzianum_GJS99.231 Trichoderma_harzianum_IMI359823 Trichoderma_harzianum_NR6883 Trichoderma_harzianum_NR6929 Trichoderma_harzianum_NR6931 Trichoderma_harzianum_NR6938 Trichoderma_harzianum_NR6950 Trichoderma_viride_BBA70239 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M827] TITLE ELF; LINK TAXA = TaxaForAnalysisStep1237; DIMENSIONS NCHAR=689; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Hypocrea_rufa_GJS99.105 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAAAAGGTAAGCTCATTTTCACTGCTTTTTT--AC--TGCG--CTTGGCA--CAATCGTGCCCGACAATTCTGTTCTCAAGTCTTGTCTCTTTTCC---TCGCAGCGTCACACCCCCGCTTTGCCTG--TCTACCCCTCCTTTGGCA-----GCAAATTTTTTCTG-CTGCCTCGTTTGAC-TTTGAGTGGGGTGCCAACTTTTTTCTTTCTTCTCCCTGGCAACCCCGCTATTGTCGCTGTCCCTCACCCATCG--------------------------------CCTCTTGACTCAATTTCTCTGTGATGCATCG-TGCTGATCATGCTT-CAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAGATACTATGTCACCGTCATCGGTATGTTATTTTCGGTCC------TTGACATGTCCAGATCATCATCATTCTAACATGCCAT--CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTGTCCTGATTATCGCAGCCGGTACTGGTGAG Hypocrea_rufa_GJS99.140 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCTCATTT-CACTGCTTTTTC--TCCCTGCG--CTTGGCA--CGATCGTGTCCGACAATTCTGTTCTCA-GTCTTGGCTATTTTCC---TCGCCGCGTCACACCCC-GCTTTGCCTG--TCTACCCCTCCTTGGGCA-----GCAAATTTTT-CTG-CTGCCTCGTTTGAC-TTTCAGTGGGGTGCCAACTTGTTTTTTTC----CCCTGGCAACCCCACTATTGTCACTGTTCCTCATCCATCGTCCCAACGATGTGCATTCCCTCAGTCGCATCGCCTCTCGACTCAATTTCTCTGTGGTTCATTG-TGCTGATCATGCTT-CAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAGATACTATGTCACCGTCATTGGTATGTTGTTTTCGGTCC------TTGACGTGTCGAGATCATCGTCATTCTAACGTGCCAC--TGCAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTGTCCTCATCATCGCTGCCGGTACTGGTGAG Hypocrea_rufa_GJS99.203 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAAAAGGTAAGCTCATTTTCACTGCTTTTTT--AC--TGCG--CTTGGCA--CAATCGTGCCCGACAATTCTGTTCTCAAGTCTTGTCTCTTTTCC---TCGCAGCGTCACACCCCCGCTTTGCCTG--TCTACCCCTCCTTTGGCA-----GCAAATTTTTTCTG-CTGCCTCGTTTGAC-TTTGAGTGGGGTGCCAACTTTTTTCTTTCTTCTCCCTGGCAACCCCGCTATTGTCGCTGTCCCTCACCCATCG--------------------------------CCTCTTGACTCAATTTCTCTGTGATGCATCG-TGCTGATCATGCTT-CAATCATTAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAGATACTATGTCACCGTCATCGGTATGTTATTTTCGGTCC------TTGACATGTCCAGATCATCATCATTCTAACATGCCAT--CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTGTCCTGATTATCGCAGCCGGTACTGGTGAG Hypocrea_sp._GJS96.132 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCCCATTACAACTTTTTTTTCCATCATTTTTTTTTTGGTATTCACGTGTGCGCGACGATTCTGTTCTCA-GCTTTGTCAATTCTTTTCACTCTCCCACAATCACCCCGCTTTGCCTG--TCTACCCCTCCTTTGGCA-TGGTGCAAAATTTTTCTGGCTGCCTTGTTTGGTTTTTTAGTGGGGTGTTTCAATTCT----TTG-----GCAGCAACCCCGCTATCGCCACTGTCCCTCATCCATCGCAACA-CAATTTGTCTCC-----ATTGCACCGTCTGCC--CTCAAATGCTTTGTGATTCATTG-TGCTGACCAGGTAT-TCAATTATAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCTGTTCTTCTCCCAGACCGCGTCTGAAGATGGCC---ATTCTAACACGCTGCTTCACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTATCCTGATTATCGCTGCCGGTACTGGTGAG Hypocrea_vinosa_GJS99.83 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCTCAATT-CA-CCCTTTTTC--ATCACGCATTTTTGGCA--CAATTGTGCTCCACGACTCTGTCCTCA-GTCTTGTCATTTCTC----TCTCAGCGTCACACCCC-GCTCTACCTG--TCTACCCCTCCTTTGGCA-CA--GCAAAAATTTTCTGGCTGCCTTGCCTGG--TTTTAGTGGGGTGCCAACTTTTT---TCTG-----GC---AACCCCGCTGTCGCC---GTCCCTCATCCATCGCCCCAACAGATTGCACTCAGTCAATCGCATCGTCTTCTGCCTCAATTTGTTT---GTTCATTG-TGCTGATCATTTTT-CAATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAGGTACTATGTCACCGTCATTGGTATGTTTTTTTCTTTCCGCTGC-TTGACACCTCCAGACCATC---CTTCTAACGTGCCAC--TACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTGTCCTGATCATCGCTGCCGGTACTGGTGAG Trichoderma_aggressivum_TH2_CBS100525 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAACTGACTTTCGCCTCGATTCTCCCTC----CACATCCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAGATTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTTTGTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTTATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_aggressivum_TH2_CBS100526 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAACTGACTTTCGCCTCGATTCTCCCTC----CACATCCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAGATTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTTTGTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTTATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_aggressivum_TH2_CBS433.95 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAACTGACTTTCGCCTCGATTCTCCCTC----CACATCCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAGATTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTTTGTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTTATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGG-GAG Trichoderma_aggressivum_TH2_CBS689.94 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAA-TGACTTTCGCCTCGATTCTCCCTC----CACATCCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAGATTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTTTGTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTTATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_aggressivum_TH4_DAOM222156 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGACAAGTTCGAGAAGGTAAGCGCCAA-TGACTTTCGCCTCGATTCTCCCTC----CACATTCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCCCGCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAATTTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTT-GTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_aggressivum_TH4_GJS99.29 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAACTGACTTTCGCCTCGATTCTCCCTC----CACATTCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCCCGCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAATTTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTT-GTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_aggressivum_TH4_GJS99.30 CTACCAGTGCGGTGGTATCGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCGCCAACTGACTTTCGCCTCGATTCTCCCTC----CACATTCAATTGTGCTCGATCATTCTGAAGAGA---ATT-----GT-CGACAATTTTT-CATCAC--CCCCGCTTTCCATT-----ACCCCTCCTTTG-CAGCGACACAAATTTTTTTTTGCTGTC--GTTTGGTTTT--AGTGGGGTTCCTTGT-------------------GCACCCCCACTAGCTCACTGCTTTTTTTT-GTGCTTCACTATCACTACCCAGCCGTCGTT--CAACGTGCTC-------TGTCTCTCGTCATCCAGTGATGCTAACCACTTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTCCTTCATCACCCCGATGCAGCAATTACAAGCCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_atroviride_GJS90.134 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTGAGCTCATTT-C--TGCTTTTTC--ACTCCGCTCCCTGAGCA--CAATCGTGCCCGACAATTCTGTCCTCA-GTCTTGTCATTTTTTTTCCTCGCAGCATCACACCCC-GCTTTACCTG--TCTACCCCTCCTTTGGCA-CA--GCAAAA-TTTTCTGGCTGCCTTGCTTGGC-TTTTAGTGGGGTGCCAACTTTTTTTGTTTG-----GCTGCAACCCCGCTATCGCGACTGTCCC---------GTCCCAACGAATTGTACTC----AATTGCATCGTCTTCT----CCATCTCTGTGTGGTTCATTG-TGCTAATCATGCTT-CAATCAATAGGAAGCCGCCGAGCTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCGCTTTTCCTCA---TTGATACTTGGAGACCAAG---ATTCTAACGTGCCGCTCTGTAGACGCTCCCGGTCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCTGACTGCGCTATCCTGATTATCGCTGCCGGTACTGGTGAG Trichoderma_atroviride_GJS95.10 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTGAGCTCATTT-C--TGCTTTTTC--ACTCCGCTTCCTGAGCA--CCATCGTGCCCGACAATTCTGTCCTCA-GTCTTGTCATTTTTCCT--TCGCAGCATCACACCCC-GCTTT-CCTG--TCTACCCCTCCTTTGGCA-CA--GCAAAAATTTTCTGGCTGCCTTGCTTGTC-TTTTAGTGGGGTGCCAACTTTTT--GTTTG-----GCTGCAACCCCGCTATCGCCACTGTCCCTC------TGTCCCAACGAATTGTACTCGCTCAATTGCATCGTCTTCTGCCTCCATCTCTGTGTGGTTCATTG-TGCTAATCATGCTT-CAATCAATAGGAAGCCGCCGAGCTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCGCTGTTCCTCA---TTGACACTTGGAGACCATC---ATTCTAACGTGCCGCTCTACAGACGCTCCCGGTCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCTGACTGCGCTATCCTGATTATCGCTGCCGGTACTGGTGAG Trichoderma_atroviride_GJS95.108 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTGAGCTCATTT-C--TGCTTTTTC--ACTCCGCTCCCTGAGCA--CAATCGTGCCCGACAATTCTGTCCTCA-GACTTGTCATTTTTTTTCCTCGCAGCATCACACCCC-GCTTTACCTG--TCTACCCCTCCTTTGGCA-CA--GCAAAA-TTTTCTGGCTGCCTTGCTTGGC-TTTTAGTGGGGTGCCAACTTTTTTTGTTTG-----GCTGCAACCCCGCTATCGCGACTGTCCC---------GTCCCAACGAATTGTACTC----AATTGCATCGTCTTCT----CCATCTCTGTGTGGTTCATTG-TGCTAATCATGCTT-CAATCAATAGGAAGCCGCCGAGCTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTTTCGCTTTTCCTCA---TTGATACTTGGAGACCAAG---ATTCTAACGTGCCGCTCTGTAGACGCTCCCGGTCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCTGACTGCGCTATCCTGATTATCGCTGCCGGTACTGGTGAG Trichoderma_harzianum_CBS226.95 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTCATTTTCGCCTCGATTCTCCCTC----CACATTTAATTGTGCCCGATAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GATTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTG-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTCGT-------------------GCACCCC-ACTAGGTCACTGCTTT-TTTT-CTGCTTCGCTCTTACTGCCCAGCCATCATT--CAACGTGCTCTG-----CGTCTCATCACTTTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATTACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_CBS227.95 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTCATTTTCGCCTCGATTCTCCCTC----CACATTTAATTGTGCCCGATAATTCTGCAGAGA---ATTTTCGTGT-CAACAATTTTT-CATCAC--CCC-GATTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTG-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTCGT-------------------GCACCCC-ACTAGGTCACTGCTTT-TTTT-CTGCTTCGCTCTTACTGCCCAGCCATCATT--CAACGTGCTCTG-----CGTCTCATCACTTTCAGCGATGCTAACCACTTTT-CCATTAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATTACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_CBS273.78 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATCCTCCCTC-TACA---TTCAATTGAACCCGACAATTCTGAAGAGA---ATTTTCGTGTTCGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTG--CTGTC--TGTTGGTTTT--AGTGGGGTTTCTTGT-------------------GCACCCC-ACTAGCTCACCTGTATTTTTC--TGCTTCACTC--ACTTCCCAGCCATCATT--CAGCGTGTTCTG-----TGTCCTTGGTCATTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTTCTTCATTAACTTCATGCTTCAATTGCAAGTCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCTGACTGCGCCATTCTCATCATTGCTGCCGGTACTGGTGAG Trichoderma_harzianum_GJS95.81 CTACCAGTGCGGTGGTATCGATCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCAATTCTCCCTC----CACATTCAATTGTGCCCGACGATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GCTTTCCGTT-----ACCCCTCCTTTGGCAGCGACGCAAATTTTTTGTGGCAGCC--TTTTGGCTTT--GGTGGGGTTTCGTGT-------------------GCACCCC-ACTAGCTCACTGCTTTTTTCT-GCTTCACTCTCCCACTGCCCAGTCATCATT--CAACGTGCTCTG-----TGTCTC--GCCATTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGCTCCATCATCTTGATGCAGGAATTGCGAGCTG-----GTGCTAACAGGTAATT-CGCAGATGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCCATTCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_GJS99.225 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATTCTTCCTC-CTCCACATTCAATTGTGCCCGACAATT-------------------------------TTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTC--GTTTGGTTTTT-AGTGGGGTTCTCTGT-------------------GCAACCCCACTAGCTC-CCTGCTTTTTCC--TGCTTCACTCTCACTTCCTCGTCATCATT--CAACGTGCTCTG-----CGTCTTTGGTCATTCAGCGACGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAAGTCT---TCACTAAGTTCATGCTGCAATTGCGGACCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_GJS99.227 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTCATTTTCACCTCAACTCTCCCTC----CACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTTTCATCAC--CCC-GCTTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTT--GTTTGGTTTT--AGTGGGGTTTCTTGT-------------------GCACCCCCACTAACTCACTGCTTTGTTTT-CTGCTTCGCTCTCACTTCCCAGCCATCATT--CAACGTGCTCTG-----TGTCTCGTCACTTTCAGCGATGCTAACCGCTTTT-CTATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATTACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_GJS99.230 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTCATTTTCGCCTCGATTCTCCCTT----CACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCTTGT-CAACAATTTTT-CATCAC--CCC-GCTTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTTGT-------------------GCACCCC-ACTAGCTCACTACTTT-TTTT-CTGCTTCGCTCTCACTTCCCAGCCATCATT--CAACGTGCTC-------CGTGTCATCACTTTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATCACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_GJS99.231 CTAC-AGTGCGT--GTATCGAC-GTCG--ACATCGAGAG--TCGAGAAGGTAAGCTTCA-CTTATTTTCGCCTCGATTCTCCCTT----CACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCTTGT-CAACAATTTTT-CATCAC--CCC-GCTTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTTGT-------------------GCACCCC-ACTAGCTCACTACTTT-TTTT-CTGCTTCGCTCTCACTTCCCAGCCATCATT--CAACGTGCTC-------CGTGTCATCACTTTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATCACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_IMI359823 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTCATTTTCGCCTCGATTCTCCCTC----CACATTTAATTGTGCCCGATAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GATTTGCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTG-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTCGT-------------------GCACCCC-ACTAGGTCACTGCTTT-TTTT-CTGCTTCGCTCTTACTGCCCAGCCATCATT--CAACGTGCTCTG-----CGTCTCATCACTTTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTTCTTTCCATCAACTTCACACAGCGATTACAAGCCA-----GTGCTAACAAGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_NR6883 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAACCTTCAACTGATTTTCGCCTCGATTCTTCCTCTCTTCACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTC-CAGCGACGCAAATTTTTTTT-TCTGTC--GTTTGGTTTTT-AGTGGGGTTCTCTGT-------------------GCAACCCCACTAGCTC-CCTGCTTTTTCC--TGCTTCACTCTCACTTCCTCGTCATCATT--CAACGTGCTCTG-----CGTCTTTGGTCATTCAGCGACGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAAGTCT---TCACTAAGTTCATGCTGCAATTGCGGACCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_NR6929 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATTCTTCCTC-CTCCACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTC--GTTTGGTTTTT-AGTGGGGTTCTTTGT-------------------GCAACCCCACTAGCTC-CCTGCTTTTTCC--TGCTTCACTCTCACTTCCTCGTCATCATT--CAACGTGCTCTG-----CGTCTTTGGTCATTCAGCGACGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAAGTCT---TCACTAAGTTCATGCTGCAATTGCGGACCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_NR6931 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATTCTCCCTC-CACACCATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAACGACGCAAATTTTTTTG-GCTGTC--GTTTGGTTTT--AGTGGGGTTTCTTGT-------------------GCACCCCCACTAGCTCACTTTTTTTTCCC-CTGCTTCACTCTCACTTCCCAGCCATCATT--CAACGTGTTCTG-----TGTCGTCACT--TTCAGCAATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTGCTCCATCAACTGCATGTTACAATTGCAGGCCA-----GTGCTAACAGTCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCTGGTACTGA-GAG Trichoderma_harzianum_NR6938 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATTCTTTCTC-CTCCACATTCAATTGTGCCCGACAATTCTTCAGAGA---ATTTTCGTGT-CGACAATTTTT-CACCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTT-GCTGTC--GTTTGGTTTTTTAGTGGGGTTCTCTGT-------------------GCAACCCCACTAGCTC-CCTGCTTTTTCC--TGCTTCACTCTCAGTTCTTCGTCATCATT--CAACGTGCTCTG-----CGTCTTTGGTCATTCAGCGATGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTTAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAGGTCT---TGACTAAGTTCATGCTGCAATTGCGGACCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTTATCATTGCCGCCGGTACTGGTGAG Trichoderma_harzianum_NR6950 CTACCAGTGCGGTGGTATCGACCGTCGTACCATCGAGAAGTTCGAGAAGGTAAGCTTCAACTGATTTTCGCCTCGATTCTTCCTC-CTCCACATTCAATTGTGCCCGACAATTCTGCAGAGA---ATTTTCGTGT-CGACAATTTTT-CATCAC--CCC-GCTTTCCATT-----ACCCCTCCTTTG-CAGCGACGCAAATTTTTTTTTGCTGTC--GTTTGGTTTTT-AGTGGGGTTCTCTGT-------------------GCAACCCCACTAGCTT-CCTGCTTTTTCC--TGCTTCACTCTCACTTCCTCGTCATCATT--CAACGTGCTCTG-----CGTCTTTGGTCATTCAGCGACGCTAACCACTTTT-CCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTAAGTCT---TCACTAAGTTCATGCTGCAATTGCGGACCA-----GTGCTAACAGGCAATT-CACAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACTTCCCAGGCCGATTGCGCTATCCTCATCATTGCCGCCGGTACTGGTGAG Trichoderma_viride_BBA70239 CTACCAGTGCGGTGGTATTGACAAGCGTACCATCGAGAAGTTCGAGAAGGTAAGCTCATTT-CACTGCTTTTTC--GCTACGCGTTCATGGCC--CAATCGTGCCCGACAATTCTGTTCTCA-GTCTTGTCAACTTTTCCC-TCGCAGCATCACACCCC-GCTTTGCCTGCCTCTACCCCTCATTTTGCA-CA--GCAAAATTTTTCTGGCAGTCTTGTTTGGC-TCTGAGTGGGGTGTCAATTTTTG----TTG-----GCAGCGACCCCGCCATCGCCACTGTCCCTCACCCATCGTCCCAACACATTGTGCTCATTCAATCGCATCGTCTTTTGCCTCAATTCCTTTGTGGTTCATTG-TGCTGATCATGTTT-CAACCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCTTTCAAGTATGCGTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCGAGACTCCCAGATACTATGTCACCGTCATTGGTATGTTTTTGGT-TCCCTCA---ATGACATTTCGCCATCATC---ATTCTAACGTGCCACTCTGCAGACGCTCCCGGCCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCTATCCTGATTATCGCTGCCGGTACTGGTGAG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = ELF) = N: 1-689; CODONPOSSET CodonPositions (CHARACTERS = ELF) = N: 1-689; END; [ The following blocks are output data for analysis step 1237 ] BEGIN TREES; TITLE Tb6013; LINK TAXA = TaxaForAnalysisStep1237; TREE Fig._2 = [&R] (((((((Trichoderma_harzianum_CBS226.95,Trichoderma_harzianum_IMI359823,Trichoderma_harzianum_CBS227.95),(Trichoderma_harzianum_GJS99.230,Trichoderma_harzianum_GJS99.231)),Trichoderma_harzianum_GJS99.227),((Trichoderma_harzianum_NR6931,Trichoderma_harzianum_CBS273.78),((Trichoderma_harzianum_GJS99.225,Trichoderma_harzianum_NR6950,Trichoderma_harzianum_NR6883,Trichoderma_harzianum_NR6929),Trichoderma_harzianum_NR6938))),Trichoderma_harzianum_GJS95.81)Trichoderma_harzianum,((Trichoderma_aggressivum_TH2_CBS689.94,Trichoderma_aggressivum_TH2_CBS100526,Trichoderma_aggressivum_TH2_CBS100525,Trichoderma_aggressivum_TH2_CBS433.95),Trichoderma_aggressivum_TH4_GJS99.29,Trichoderma_aggressivum_TH4_GJS99.30,Trichoderma_aggressivum_TH4_DAOM222156)Trichoderma_aggressivum),((((((Trichoderma_atroviride_GJS90.134,Trichoderma_atroviride_GJS95.108),Trichoderma_atroviride_GJS95.10)Trichoderma_atroviride,Trichoderma_viride_BBA70239),((Hypocrea_rufa_GJS99.105,Hypocrea_rufa_GJS99.203),Hypocrea_rufa_GJS99.140)),Hypocrea_vinosa_GJS99.83),Hypocrea_sp._GJS96.132))Trichoderma; [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5619] END;