#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 April 25, 2024; 12:54 GMT TreeBASE (cc) 1994-2008 Study reference: Chaverri P., Samuels G., & Stewart E. 2000. Hypocrea virens sp. nov., the teleomorph of Trichoderma virens. Mycologia, 93(6): 1113-1124. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S857] [ The following blocks are input data for analysis step 1419 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1419; DIMENSIONS NTAX=7; TAXLABELS Hypocrea_flavovirens_PC4 Hypocrea_nigricans_GJS98.183 Hypocrea_virens_GJS95.194 Trichoderma_virens_GL20 Trichoderma_virens_GL21 Trichoderma_virens_GL3 Trichoderma_virens_GL39 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M311] TITLE 'ITS tef-1'; LINK TAXA = TaxaForAnalysisStep1419; DIMENSIONS NCHAR=1566; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080 1090 1100 1110 1120 1130 1140 1150 1160 1170 1180 1190 1200 1210 1220 1230 1240 1250 1260 1270 1280 1290 1300 1310 1320 1330 1340 1350 1360 1370 1380 1390 1400 1410 1420 1430 1440 1450 1460 1470 1480 1490 1500 1510 1520 1530 1540 1550 1560 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Hypocrea_flavovirens_PC4 ----------------------CCTCCGTAGGGTGAACCTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGG-AAAAACAACCAAAACTCTTTTGTATACCCCCTCGCGGGTTTTCTTACT-TCTGAGAACTTCTCGGCGCCCCTTAGCGG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTCCCTTCGCGGGGCGGCCGGCCCCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCAATGCCGT-AAA-ACACCCAACTTT--------------------------------------------------------------CC-ACGTGGTCGTTATCGTATGTATTCACCAGATTCCTTTCGGCATCATTCGCCGATTTGTCGTTTGAAACAATTGTGCTAACTGT-TGCTTTCCAGGGGTGCGTATTCCATC---TATCGTGAAGGACATCGATCGAACACA--TCACTGACCTAC-TACGACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCCATTC--CCTGACATGCCATCAAGCCATAGTGCT--TGATGGGGGACATC-ACCTCTTTGA-ACTCTGCGCTGACCATCTTCTTCACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACCGT-CGTACCATC-GAGAAGTTCGAGAAGGTAAGC-TCAATCAACTGATTCCGACTCTGGTTT---TCCGTTCCCCTTCAATT-GTGACGGACAATTC-TCAACCGGAATTAT-CCTTGTCAACAATTTTG--CATCACCCCG--CTTTCTCTTCCCATTACCCCTCCTTTGCA-GCG-ACGCAAA---TTTTTTTGCAGCC--TC--GAATTTT---AGTGGGGTCGCTTGTGCATCCCCCACCAACCATTCACTGCTTTTGCCCTTGACTGCGTGTACCTGTCATCATTCCACGCTTTTCGTCATC----TCTTTCAGCGATGCTAACCATCTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTACGGATCTCATCCCGTTCCTTGTTCGCCAGCCTGTACTAATGCCAGTTTGACAGACGCTCCCGGC--------------- Hypocrea_nigricans_GJS98.183 ----------------------CCCTCCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTTTATAATCTGAGC-CTTCTCGGCGCCTCTCGTA-G--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTGCCTTGGCGGTGGCCGTCT--CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTT-AA-ACACCCAACTT------------------------------------------------------------------------TCGT-A-CGTAC-AATCCTGTTCCCTCACGTCGGCATCATTCGCCGGTCTGAT-TCTCAAACACTTGTGCTAACCAT-CGCCTTCTAGGGGTGCGTATTCCATCAATCATCTTGAATGAGATCGATCGAACACA--ATACTGACTTGC-TATAACAGCCACGTCGACTCCGGAAAGTCGACCACCGTAAGTTG-CACCCTCT----CTTGCTCCGATATCAAACGT---CGTT--TGATGGGGGACACCTAC--TCTAGA-GCACAGGGCTAACCATTCATCATACAGACCGGTCACTTGATCTACCAGTGCGGTGGTATC-GACCGT-CGTACCATC-GAGAAGTTCGAGAAGGTAAGCTTCAACTGATT--TTTCGCCTCGATTCTTTCCTCCTTCACATTCAATT-GTGCCCGACAATT--CTGCAGAGAATTTT-CGTGT-CGACAATTTTT--CATCACCCCG--CTTTCCGTT------ACCCCTCCTTTGCA-GCG-ACGCAAAA-TTTTTTTTGCTGTCG-TCT-GGTTTTT---AGTGGGGTTCTCTGTG---------CAACCCCACTAGCTCACTGCTTTTTCCTGCTTCACTCTCACTTCCTCGTCATCATTCAACACGCTCTGTGTCTTTGGTCATTCAGCGATGCTAACCACTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTTCATCAATCTCATGGTGCAACTGCGAGCTAGTGCTAACATGCAATTTCACAGACGTTTCCCGGGCACCGTGA Hypocrea_virens_GJS95.194 T---------------------------------------GCGGAGGGATCATTACCGAGTTTACAA-TCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTC--------------------------------------------------------------------------------TAT-TATCCCAC-CACTTTCGTCGGCATCGTCCGCCGCTCTGAC-TCTAGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATAAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCGACGTCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAATT-GTGCTCGACAATTC-TGTTCAAGAATCAT-CGAGG-CAACAATTTTTT-CGTCCCCCCG--CTTTCG-TTCCATTACCCCCTCCTTTGCAAGCG-ACGCAAAAA--TTTTTTGCTGCC--TCT--GGTTTTTT-AGTGGGGGG--TTGCACCAG------CAACCCCCACCCACTTTCCTTGGTGGCTCTTTGCC-CCTTCGTCTTACCCAACTTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trichoderma_virens_GL20 TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA--------------TTCCTAT-TATCCCAC-CACTTTCGTCGGCATCGTCCGCCGCTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAAT--GTGCTCGACAATTC-TGGTCA-GAATCAT-CGAGGGCAACAATTTTTT-CGTCACCCCG--CTTTCGGTTCCATTTACCCCTCCTTTGCA-GCG-ACGCAAAAAATTTTTTTGCTGCCCTTT--GGGTTTTTTAAGTGGGGGGG--TGCACC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trichoderma_virens_GL21 ---------------------GGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTC-------------------------------------------------------------------------------------------------------------GTCCGCCGCTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAG-TAACCATACGCCATACAGACTGGTCACTTGATCTACCAGTGCGGGGGTATC-GACAAG-CGTACCATCCGAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCAT-AATTT----CCCCTTCACATTCAATTGGTGCTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trichoderma_virens_GL3 TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA------------------TAT-TATCCCA--CCGTTTCGTCGGCATCATCCGCCGCTCTGAC-TCTGGAATCTTTGTGCTAACAAC-CGTCCTCTAGGGGTACGTATTCCGTCAATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCGACGTCAAACGTTGCCGTT--TGATGCGGGGTGTCTACGCTTTTGA-ACACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATCAGACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTAAGCT-CAATCAACTGGTTTCGCATCAATTT----CCCCTTCCCATTCAATT-GTGCTCGACAATTT-CTGTTCAGAATCAT-CCGATGCAACAATTTTTT-CGTCACCCCG--CTTTTCGTTCCCATTACCCCTCCTTTGCA-GCG-ACGCAAAAA-TTTTTTTGCTGGCCTTCT-GGGTTTTT--AGTGGGGGGG--TGCAACCAAG---CCAACCCCCACCACTTGCCTTTTTTTGCTTTTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Trichoderma_virens_GL39 TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA----------------------------------------CGGCATCGTCCGCCGTTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGCCGACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGAGGTATCTGACAAGGCGTACCATC-GAGAAGTTCGAGAAGGTGAGCCTCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAATTTGTGCTCGACAATTT-TGTTTA-GAATCAT-CGAGGGCAACAATTTTTTTCGTCACCCCGGCTTTTTGTTCCCATTACCCCTCCTTTTGCCAGCGGACGCAAAAATTTTTTTGGCTGCC--TCT-GGGTCTTAT-AGTGGGGGGG-TTGCAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN SETS; CHARSET TEF (CHARACTERS = 'ITS tef-1') = 659-1566; CHARSET ITS (CHARACTERS = 'ITS tef-1') = 1-658; CHARSET EXON3 (CHARACTERS = 'ITS tef-1') = 954-1026; CHARSET EXON1 (CHARACTERS = 'ITS tef-1') = 659-676; CHARSET EXON2 (CHARACTERS = 'ITS tef-1') = 824-857; CHARSET INTRON1 (CHARACTERS = 'ITS tef-1') = 677-823; CHARSET INTRON3 (CHARACTERS = 'ITS tef-1') = 1027-1566; CHARSET INTRON2 (CHARACTERS = 'ITS tef-1') = 858-953; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS tef-1') = N: 1-1566; CODONPOSSET CodonPositions (CHARACTERS = 'ITS tef-1') = N: 1-1566; END; [ The following blocks are output data for analysis step 1419 ] BEGIN TREES; TITLE Tb6195; LINK TAXA = TaxaForAnalysisStep1419; TREE Fig._2 = [&R] (((Hypocrea_virens_GJS95.194,Trichoderma_virens_GL3,Trichoderma_virens_GL20,Trichoderma_virens_GL21,Trichoderma_virens_GL39),Hypocrea_nigricans_GJS98.183),Hypocrea_flavovirens_PC4); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3992] END;