#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 27, 2024; 21:21 GMT TreeBASE (cc) 1994-2008 Study reference: Bakkeren G., Kronstad J., & Levesque C. 2000. Comparison of AFLP fingerprints and ITS sequences as phylogenetic markers in Ustilaginomycetes. Mycologia, 92: 510-521. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S642] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=12; TAXLABELS 'Ustilago aegilopsidis #4327 MAT-1' 'Ustilago avenae #A-60 MAT-1' 'Ustilago bullata #B-249 MAT-2' 'Ustilago hordei 316 #14.1 MAT-2' 'Ustilago hordei 362 #4854 MAT-2' 'Ustilago hordei 364 #4857 MAT-1' 'Ustilago hordei 521 #4640 MAT-2' 'Ustilago hordei 523 #4632 MAT-2' 'Ustilago kolleri #K-45 MAT-1' 'Ustilago nigra #83-138 MAT-2' 'Ustilago nuda #96-253' 'Ustilago tritici #T-2' ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=15; TAXLABELS Puccinia_caricina_#U88234 Sporisorium_reilianum Tilletia_indica_#11 Tilletia_walkeri_#M96442 'Ustilago aegilopsidis #4327 MAT-1' 'Ustilago avenae #A-60 MAT-1' 'Ustilago bullata #B-249 MAT-2' 'Ustilago hordei 316 #14.1 MAT-2' 'Ustilago hordei 362 #4854 MAT-2' 'Ustilago kolleri #K-45 MAT-1' Ustilago_maydis_#521_a1b1 'Ustilago nigra #83-138 MAT-2' 'Ustilago nuda #96-253' 'Ustilago scitaminea #5 MAT-2' 'Ustilago tritici #T-2' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2584] TITLE 'ITS1-5.8S rRNA-ITS2'; LINK TAXA = Taxa2; DIMENSIONS NCHAR=805; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Puccinia_caricina_#U88234 CC-TGC-A--GAAGGATCATTATTTAAACAAGAGT-GCACTTAATTGTGGCTC-AACCTTTTTATAA--TTTCACCCCAACACTTGGTTGTGTGATAGAACTTGTTTTTGTCATTGCAATCAGGT--AGAAGTAACACTTTTG-------TT--GCATT---ACCCCCCCTCAATTATTTTAA---AACACAAGT--------T--GAA--TT--AAG----AATG---------------TAAAA--TTTTG-----------AT---AAATTGAAATAACTTTTAACTTTTAACAATGGATCTCTTGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATCCAGTGAATCATTGAATCTTTGAACGCATCTTGCACCTTTTG-----GTATTCCAAAAGGTACACCTGTTTGAGTGTC-ATGAAAATCT---CTCACA---A-----------------ATTAATT---TTTGGTGGATG-----TTGAGTGTTGCTGCTATCTA-----GCTCAGTTTAAATATATAAGTCTCATTCTACATGT-TG------GATTGACTTGGTGT-AAT-ATTT----------AATTTTTT-TTTCATCAA--GGATT-AG----TAGCAATACT----------TGCCAATGTTT-------TAGAAC------AGGGAC--TGCT------AAACCCATTATAA------T--T--CTT--------------TTTTTTTAT----A---AG------------ACCTCAAATCAGGTGGGAC Sporisorium_reilianum CATTTCGA-TGAAAAAACCTTTTTTTCTGAGGTGCGGCCCGCACCTGTCCAACTAAACTAGGGCTACTTTTTT----CAACAC---------GGTTGCATC--GGTTGGGTTGGGTCGAGCGAGT--TTTC--------GGA---------CTCGT------GAGGCCGGCCTGACAACTTAACAAAACACTTTT-GATGATCTAGGAATTTTGAAAG--------TC-TATCTT------TGAA--CGGCTGGTAATGCGGTCGTCTAAAAATGGAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCTGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACC-CA-CGCTTTTTTA--AGT---AAA-------GGCGTGCGGGATCGG-TAGTGAGGG--T-TGCCATTCACCGTGGCTCGCTCGAAATGCATTAGCGCATCCATTGAATTGAGGC-AAAGACGGACGAAGGCTCGC--CTTT------------CGCTCTCTCTTCCTTGCCGGGTTTTGATACTATCAGGGCTTCGGAG--GCGGAGAGAGGGCATG-AGCTGG-ACGC---GAC-GACTTTGTCGGTTGGAAGTGCTTCTGAACCCCGCC-----------------TTTGGCATTTATTTGCCAA---AGGAA-------TTAATTCAA---A--TCGGCC Tilletia_indica_#11 CC-TGC-A--GAAGGATCATTAGTGAATTACG-GA-GCTCTT--CTTCGGAAG-AGTCTCCTTCT-C--TTTTATCCCAACACCAAACTAC-GGAAGGAACGAGGCCTTG-CGCTGAGTACCTGTCCGGATGGAACAGAGTTGCTGGTACTTCGGTATTGGCAGCGCTGCTCCAACCCTTTTA---AACAC---T--------TAAGAA--TT-AAAG----AATG---------------TTAAAGCTATTG--TCTTCGGACAT---AAACT--AATA---TACAACTTTTGACAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCTTGG-----GTATTCTCAAGGGCATGCCTGTTTGAGTGTC-ATAATACTCTCAACTCTCA---ATCTTTTTGTAAGAGAAGATTGCTTGGAGTTGGT-GATGGGCGCTTGCCAGATGTAACAGTCTT-----GCTCGCCTTAAATTAATCAGTGGATCTCTTCGAGTCCG------GTCTGACTATGTGT-GATAATTTGATCACATAGAATGTGCT-TGTCA-CAACCGGATTCTG----TATAGAGGCT---------CTGC-------T-------TCCAAC------ACGGAA--TG----------ATTCTTCGGAA------TCAT--CGA--------------TAGCTTTGT----AGCTTG------------ACCTCAAATCAGGTAGGAC Tilletia_walkeri_#M96442 CC-TGC-A--GAAGGATCATTAGTGAATTACG-GA-GCTCTT--CTTCGGAAG-AGTCTCCTTCT-C--TTTTATCCCAACACCAAACTAC-GGAAGGAACAAGGCCTTG-CGCTGAGTACCTGTCCGGATGGAACAGAGTTGCTAGTACTTCGGTATTGGCAGCGCTGCTCCAACCCTTTTA---AACAC---T--------TAAGAA--TT-AAAG----AATG---------------TTAAAACTATTG--TCTTCGGACAT---AAACT--AATA---TACAACTTTTGACAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCTTGG-----GTATTCTCAAGGGCATGCCTGTTTGAGTGTC-ATAATACTCTCAACTCTCA---ATCTTTTTGTAAGAGAAGATTGCTTGGAGTTGGT-GATGGGCGCTTGCCAGATGTAACAGTCTT-----GCTCGCCTTAAATTAATCAGTGGATCTCTTCGAGTCCG------GTCTGACTATGTGT-GATAATTTGATCACATAGAATGTGCT-TGTCA-CAACCGGATTCTG----TATAGAGGCT---------CTGC-------T-------TCCAAC------ACGGAA--TG----------ATTCTTCGGAA------TCAT--CGA--------------TAGCTTTG-----AGCTTG------------ACCTCAAATCAGGTAGGAC 'Ustilago aegilopsidis #4327 MAT-1' CATTTCGA-TGAAAAACC-TTTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAGTTTATTTTTATTTTATTATTATAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago avenae #A-60 MAT-1' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACAA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG-----------TTTTTTTTTTTAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago bullata #B-249 MAT-2' CATTTCGA-TGAAAACCC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACCTTTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTTGCGTCTGCTGGGCGACGGACGGACAATTTTATTTAACACTTTTGGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGGAAAAA-------G-GTTGACGGATCGG-TATTGAGGGGTTTTGCCATTTACCGTGGCTCCCTCGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTGG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG--------------TTTTTTTTAGGAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago hordei 316 #14.1 MAT-2' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG------TTTATTTTATT-TTATAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago hordei 362 #4854 MAT-2' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG------TTTATTTTATT-TTATAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago kolleri #K-45 MAT-1' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAGGTCATTTTTACAA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG-----------TTTTTTTTTTTAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC Ustilago_maydis_#521_a1b1 CATTTCGA-TGAAAAACCTTTTTTTTCTGAGGTGTGGCTCGCACCTGTCCAACTAAACCTGAGCTACCTTTTTTATATAACAC---------GGTTGCATC--GG-TCGGTCTGTCGAAACCAGTAGCG-CTCAT----AGCGAGCA-----GCGTCTGGGGAAAGACGGGTCGGCGCTTCTTACCAACACTTTT-GAACA-CTAGGA--TTGGAAGGACAAAAA-TCATTTTTTTGATGATGGAAGCGACTGGTAATGCGGTCGTCT-AAATTGAAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATTTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGCTTTTTTTTCTTGTTGAGAAA-------GAGCTGGCGGATCGG-TAGTGAGGGTCTCTGCCATTTACCGTGGCTCCCTCGAAATGCATTAGCGCATCCATTGGA---AGGCGGAAGACGGACGAAAGCTCGAGTTTTT------------TGCCCTCGCTTCCCTGCCGGGTTTTGATAATGTCAGGACTTCGGAG-CGAAGAG-A-GGGCG-GGAGCTGGAACGCACGAACTT-TTCTGCTGTTTGGGCGTGCTTCTGAACCCCGCCCATGCC----------------TCTTGCTTTACCCCAGAAGGAAGGGATTTATTTTTCAATTCA--TCGGCC 'Ustilago nigra #83-138 MAT-2' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG------TTTATTTTATT-TTATAGAAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC 'Ustilago nuda #96-253' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACC-TTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGC-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACAGACAATTTTATTGAACACTTTTTGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTATCGTGGCTCCCTTGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTCG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG-------------TTTTCTTTTAGAAAGCTAGGAAGGAATTTATAAT--AATTCA--TCGGCC 'Ustilago scitaminea #5 MAT-2' CATTTCGAGTGAAA--CC--TTTTTTCCGAGGTGTGGCTCGCACCTGTCTAACTAAACT-GGGCTACCTATTT----CAACAC---------GGTTGCATC--GGTTGGGTCTG--CCAAACAGT--GCACGAAA----GTA---------CCTGT------GGAGGCAGCCCGATAATCTACCAAAACACTTTT-GATGGTCTAGGA--TTTGAAAG-----------TATTTAACAT--TTTA--CGACTGGTAATGCGGTCGTCTAAAATCTAAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGCAGATCTAATCTGGGGAGCATGCCTATTTGAGGGCCGCGAATTGTTTCGAACG-CA-CGCTTTTTTATTACG---AAA-------GAGCTGGCGGATCGG-TAGTGAGGGTTT-TGCCATTTACCGTGGCTCCCTCGAAATGCATTAGTGCATCCATTTGA--CAGGC-AAAGACGGACGAAGGCTCGA--CTTT------------TGGCCCATCTTCCCTGCCAGGTTTTGATAATATCAGGACTTTGGTG--G-TGAGGATGAGCAAGAAGCTGG-ACGC---GACGGCCTTTGCTGATTGG-AGTGCTTCTGAACACCGCCCTAGCTAA----TTTTTTATTTTATTTTTTTGGCTA---GGGAA--------TAATTCAA---A--TCGGCC 'Ustilago tritici #T-2' CATTTCGA-TGAAAAACC--TTTTTTCAGAGGTGTGGCTCGCACCTGTCCAACTAAACTTGAGCTACCTTTTTT---CAACAC---------GGTTGCATC--GG-TCGGCCTGTC--AAACAGT-GCGACGCAA----GGAGAAAATCCTCGCGTCTGCTGGGCGACGGACGGACAATTTTATTTAACACTTTTGGATGATCTAGGA--TTTGAAGGAGAAAAAGTCATTTTTACGA--ATGAAATCGACTGGTAATGCGGTCGTCT--AATTTTAAAA----ACAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCGGCAGATCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGAATTGTTTCGAACGACAGC--TTTTTTCTTTTGG-AAAA-------G-GTTGACGGATCGG-TATTGAGGGTTTTTGCCATTTACCGTGGCTCCCTCGAAATAGATTAGCGCATCCATTTTAT--AGGC--AAGACGGACGAAAGCTCGA--TTTT------------TGCTCTCTCTTCCCTGCCGGGTTTTGATACTATCAGGACTTCGGAGAGGTTGAG-ATGGGTA-GGAGCTGG-ACGC---AACGG-CT-TGCTGTTT-GGAGTGCTTCTGAAACCCGCCCATGCCGAG----------------TTTTTTAGGAAGCTAGGAAGGGATTTATAAT--AATTCA--TCGGCC ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1-5.8S rRNA-ITS2') = N: 1-805; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1-5.8S rRNA-ITS2') = N: 1-805; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2630] TITLE AFLP; LINK TAXA = Taxa1; DIMENSIONS NCHAR=207; FORMAT DATATYPE=Standard SYMBOLS= "0 1" MISSING=? GAP= -; CHARSTATELABELS 1 'BamP.aa + MseP.c, size 97', 2 'BamP.aa + MseP.c, size 99', 3 'BamP.aa + MseP.c, size 108', 4 'BamP.aa + MseP.c, size 111', 5 'BamP.aa + MseP.c, size 113', 6 'BamP.aa + MseP.c, size 115', 7 'BamP.aa + MseP.c, size 118', 8 'BamP.aa + MseP.c, size 124', 9 'BamP.aa + MseP.c, size 140', 10 'BamP.aa + MseP.c, size 142', 11 'BamP.aa + MseP.c, size 144', 12 'BamP.aa + MseP.c, size 146', 13 'BamP.aa + MseP.c, size 147', 14 'BamP.aa + MseP.c, size 148', 15 'BamP.aa + MseP.c, size 150', 16 'BamP.aa + MseP.c, size 164', 17 'BamP.aa + MseP.c, size 182', 18 'BamP.aa + MseP.c, size 184', 19 'BamP.aa + MseP.c, size 193', 20 'BamP.aa + MseP.c, size 198', 21 'BamP.aa + MseP.c, size 208', 22 'BamP.aa + MseP.c, size 216', 23 'BamP.aa + MseP.c, size 218', 24 'BamP.aa + MseP.c, size 220', 25 'BamP.aa + MseP.c, size 222', 26 'BamP.aa + MseP.c, size 235', 27 'BamP.aa + MseP.c, size 237', 28 'BamP.aa + MseP.c, size 239', 29 'BamP.aa + MseP.c, size 252', 30 'BamP.aa + MseP.c, size 256', 31 'BamP.aa + MseP.c, size 260', 32 'BamP.aa + MseP.c, size 291', 33 'BamP.aa + MseP.c, size 303', 34 'BamP.aa + MseP.c, size 316', 35 'BamP.aa + MseP.c, size 319', 36 'BamP.aa + MseP.c, size 322', 37 'BamP.aa + MseP.c, size 325', 38 'BamP.aa + MseP.c, size 336', 39 'BamP.aa + MseP.c, size 342', 40 'BamP.aa + MseP.c, size 399', 41 'BamP.aa + MseP.c, size 402', 42 'BamP.aa + MseP.c, size 403', 43 'BamP.aa + MseP.c, size 420', 44 'BamP.aa + MseP.c, size 425', 45 'BamP.aa + MseP.c, size 430', 46 'BamP.aa + MseP.c, size 434', 47 'BamP.aa + MseP.c, size 437', 48 'BamP.aa + MseP.c, size 438', 49 'BamP.aa + MseP.c, size 455', 50 'BamP.aa + MseP.c, size 465', 51 'BamP.aa + MseP.c, size 468', 52 'BamP.aa + MseP.c, size 470', 53 'BamP.aa + MseP.c, size 472', 54 'BamP.aa + MseP.c, size 478', 55 'BamP.aa + MseP.c, size 481', 56 'BamP.aa + MseP.c, size 490', 57 'BamP.aa + MseP.t, size 66', 58 'BamP.aa + MseP.t, size 69', 59 'BamP.aa + MseP.t, size 93', 60 'BamP.aa + MseP.t, size 95', 61 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130 140 150 160 170 180 190 200 ] [ . . . . . . . . . . . . . . . . . . . . ] 'Ustilago aegilopsidis #4327 MAT-1' 110100001010001100011001100011101110000000010010010011010010001000000010110010000100010000110010110011000011110110000011010010000000000000000001011100011010111000101010100010101101000000010010101110001100101 'Ustilago avenae #A-60 MAT-1' 010101001010001100011001100011100111000000010010110001000000001101010010110010000111011000010000110010111001110111000011010110010010010100000101100100011010110000101001100011101111000000011010001111100000111 'Ustilago bullata #B-249 MAT-2' 011110100010001101011110110011100100100101011111010000001010000010100001011000001010100011010000010000000101011110111011100000101001000010000011000110101110001010011000101010111000000000110010001010010000101 'Ustilago hordei 316 #14.1 MAT-2' 110100011010001100011001100011101110010010100010010011010110001000000110110111100110010000111110110001000011110110000011010010000000001000000001011101011011111000101010100010101101100010010010101110000100101 'Ustilago hordei 362 #4854 MAT-2' 110100011010001100010001100011101110010010100010010101110110001000000110110111100110010000111111110001100011110110000011010010000000000000010001111100011011111000101010100010101101100010010010101110001100101 'Ustilago hordei 364 #4857 MAT-1' 110101011010001100010001100011101110010010100011010101110010001000000110110111100110010000110101111001100001110110000011010010000000001001010001011100011011111000101000100010101101010000010010101110001100101 'Ustilago hordei 521 #4640 MAT-2' 110100011010001100010001100111101110010010100011010011010110001000000110110111100110010000111110110001000011110110000011011010000000000000010001011101011011111000101010100010101101000000010010101110001100101 'Ustilago hordei 523 #4632 MAT-2' 110100011010001100010001100011101110000010100010010011010010001000000110110111100110010000110100110001000011110110000011010110000000000000000001011101011011101000101010100010101101000110010010101110001100101 'Ustilago kolleri #K-45 MAT-1' 110101001010001100011001100011110111001000010010111001010000001101010010110010000111010100110000110000100001110110001011010011010000010000000101110101011010110000101001100011101101000000011110001111100000111 'Ustilago nigra #83-138 MAT-2' 110100011010001100011001101011101110000010100010010011010110001000000010110110000110010000110110111001000011110110000011010010000000000000000001011101011011111000101010100010101101000010010010101110001100101 'Ustilago nuda #96-253' 110000000100111100100001100001110100000001011011000001011010111000001001000000010010000000100001111100000001110111000111010000000000010000000000001011001010101000101101110010101001101000010001011110000011101 'Ustilago tritici #T-2' 010000001011001110010110100011100100010000001010100001010011001000000001000000010011100001000100011000101001110111000001100000000101100000101010000001000110001111111000110111101001001001010011001010000010100 ; END; BEGIN TREES; TITLE Tb5731; LINK TAXA = Taxa2; TRANSLATE 1 'Ustilago bullata #B-249 MAT-2', 2 'Ustilago tritici #T-2', 3 'Ustilago avenae #A-60 MAT-1', 4 'Ustilago kolleri #K-45 MAT-1', 5 'Ustilago hordei 316 #14.1 MAT-2', 6 'Ustilago hordei 362 #4854 MAT-2', 7 'Ustilago nigra #83-138 MAT-2', 8 'Ustilago aegilopsidis #4327 MAT-1', 9 'Ustilago nuda #96-253', 10 Ustilago_maydis_#521_a1b1, 11 Sporisorium_reilianum, 12 'Ustilago scitaminea #5 MAT-2', 13 Tilletia_walkeri_#M96442, 14 Tilletia_indica_#11, 15 Puccinia_caricina_#U88234; TREE Fig._2_ITS = [&R] ((((((1,2),((3,4),(5,6,7,8),9)),10),11),12),((13,14)Tilletia,15))Ustilaginomycetes; END; BEGIN TREES; TITLE Tb5732; LINK TAXA = Taxa1; TRANSLATE 1 'Ustilago aegilopsidis #4327 MAT-1', 2 'Ustilago avenae #A-60 MAT-1', 3 'Ustilago bullata #B-249 MAT-2', 4 'Ustilago kolleri #K-45 MAT-1', 5 'Ustilago nigra #83-138 MAT-2', 6 'Ustilago nuda #96-253', 7 'Ustilago tritici #T-2', 8 'Ustilago hordei 316 #14.1 MAT-2', 9 'Ustilago hordei 362 #4854 MAT-2', 10 'Ustilago hordei 364 #4857 MAT-1', 11 'Ustilago hordei 521 #4640 MAT-2', 12 'Ustilago hordei 523 #4632 MAT-2'; TREE Fig._2_AFLP = [&R] ((((1,(5,((8,((9,10),11)),12)Ustilago_hordei)),(2,4)),6),(3,7))Ustilago; END;