#NEXUS [written Thu Jan 19 18:00:05 JST 2017 by Mesquite version 3.2 (build 801) at C215-MacBookPro.local/10.40.106.14] BEGIN TAXA; TITLE Uromyces_japonicus_phylogeny; DIMENSIONS NTAX=24; TAXLABELS Puccinia_allii_LC203757 Puccinia_allii_AF511077 Puccinia_allii_KU296877 Puccinia_allii_KU296882 Puccinia_allii_KU296883 Puccinia_allii_LC203756 Puccinia_allii_KU296869 Puccinia_andropogonis_EF583818 Puccinia_asparagi_AY217137 Puccinia_hordei_AY874150 Puccinia_mixta_KU296895 Puccinia_obscura_AF468042 Puccinia_porri_AF511073 Puccinia_porri_KU296909 Puccinia_striiformis_EU014048 Uromyces_durus_LC203758 Uromyces_erythronii_LC203755 Uromyces_japonicus_LC203759 Uromyces_japonicus_LC203760 Uromyces_japonicus_LC203761 Uromyces_japonicus_LC203762 Uromyces_reichertii_AF511084 Uromyces_scillarum_AF511085 Uromyces_striatus_FJ468409 ; END; BEGIN CHARACTERS; TITLE Uromyces_japonicus_phylogeny; DIMENSIONS NCHAR=764; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Puccinia_allii_LC203757 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTT-----------------TTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_AF511077 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTTTT-------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAAAAAAACCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_KU296877 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTTT--------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATYGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_KU296882 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTTT--------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAARACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_KU296883 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTTT--------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_LC203756 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTTT--------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_allii_KU296869 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCCTCTTCTTTTTTTT-------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAAAA---CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_andropogonis_EF583818 GATCATTATTAAAAGAACTAGAGTGCACTTGATTGTGGC-TCGACCCCTTTT-----AAA------CTCACCCAAAC--TTTTAAAGA-CTCTTTTGCATGATTTTGAGAAAAATCATTGCATCTGAGTAAAAGTAAC-TTCTTAATTGAAT-GTTACATTACCC-TCCCCCTTTTATTTTTCCAAAACTTTTTTTTT-ATT-TAATTTATACA---CACAAGTTTAAAA---GAATGTAAACAACCAC--------AATTATAAAATATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAAATAATTTT------ATT-ATTATT-CTTTGTGGATGTTGAGTGCTGCTGTGTT-TA-------GCTCACTTTAAATATATAAGTTATCTTCTTG----AACAAATAAGT-GA-AAGTTGGATTGACTTGGTGTGTAATAAT--TTTTT-C-ATCACATCAAGGAAAGTAG-TAA-TACTTGCCATCTTTATATATT-ATTTT-GTTGTTGAGATAGAGACTTCTAAA--CAAACAAAC----ATA-A-----------CTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_asparagi_AY217137 GATCATTATTAAAAGAACTAGAGTSCACTTAATTGTGGC-TCGACSCCTTTT-----AAAC-CA-TCTCACCCAAAC--TTTTAAAGA-CTCTTTTGCATGATTT-GA-AAGAATCATTGCACCTGAGTAGAAGTAAC-TTCTTAATTGAAT-GTTACATTACCCCCCCCTTTT--ATTCTTCCAACCTTTTTTTTTTTTTT-T-ATA-ACACA---CACAAGTTTAAAA---GAATGTAAAAAACCA---CCTTT-AATTATAAAA----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAAATAATTTT------ATT-ATTATT-CTTTGTGGATGTTGAGTGCTGCTGTGTT-CACAACACAGCTCACTTTAAATATATAAGTTATCTTCTTACTTTGACAAAAAAAAAGTTAAGCTGGATTGACTTGGTGTGTAATAAT--TTT---C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTTTGT--ATT-ATTTTTGTTGTTGAGCAAGAGACTTCCAAA--CAAAA---TCCA-A-ATCAAT--------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_hordei_AY874150 GATCATTATTAAAAGAACTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAT--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCCTTTTTTTTTTT---------------TT--TTATA-ATTAA---CACAAGTTTAAAT---GAATGTAAAA--CAA---CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATAGTTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTAAAT---------A-AAAGGGACTTCTAAAAA--------CCC--A-ATTAATTATT----TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_mixta_KU296895 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTTTT-AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTTT----------------TTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAAA-----CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAAAAA--CCCCCA-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_obscura_AF468042 GATCATTATTTATAAAAATGGAGTGCACTTAATTGTGGC-TCTGATCTTTTT-------ATATCATCTTACCCCAA----AACTT-G-TTTGTGTGACATC-TTT--A--GGTGTCATTGCACTCAGGTATACGTAAC-AG-TT--CTGT-T-ACATTACCCCCCCCACCCC---------------AATTTTTTT---ATTTTTTTTTATCAA---CACAAGTTTAAATTAAGAATGTAAA---CA-----TTTTAAATTATGAAAA---TAACTTTTAACAATGGATCTCTAGGCTCTCATATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATTGAATCTTTGAACGCACCTTGCACCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAAATCTCTCATCAAATTAATT-------------------TTTGGTGGATGTTGAGTGCTGCTGTTATCTA-------GCTCACTTTAAATATATAAGT---CTTTTTC-------------TAATTA-TGTTGGATTGACTTGGTGT--AATAATTATTTT---GATCA--TCAAGGAAAGTAG-CAA-TACTTGCCAAT-------GTTTT----------GGA-CAAAGGACTCCTAAATTGAT------------ATTATATTTTTA-TTTTTAAGACCTCAAATCAGGTGGGACTACCTGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_porri_AF511073 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTTTT-AAA-----TCTTACCCAAAC--TAACTAAGG-CT-TTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCCCTCCTCTTCTTTTTT---------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAA-CAAAA-CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCACCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGTTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTAAAC---------A-AAAGGGACTTCTAAA----------CCCC-A-ATTAATTACC----TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_porri_KU296909 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTTTT-AAA-----TCTTACCCAAAC--TAACTAAGG-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCCCTCCTCTTCTTTTTT---------------ATTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAA-CAAAA-CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCACCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGTTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTAAAC---------A-AAAGGGACTTCTAAA----------CCCC-A-ATTAATTACC----TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Puccinia_striiformis_EU014048 GATCATTATTAAAAGAACTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTT----AAAA-A---TCTCACCCAAAC--T-TTTAAGA-CTTGGTTGCATGATTT-GA-AAGAATCATTGCAATTGAGTAGACGTAAC-TTCTTTATTGAAT-GTTGCATTACCC-TCCCTTTTTT--TTTTTTTT-------------ATTAAAAATTACACAAAACACAAGTTTAAAT---GAATGTAA----CCAAA-CCTTT-AATTATAAA-----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAA-TAATTTT-----GATTAATTATTTTCAA-TGGATGTTGAGTGCTGCTGTAAT-TA-------GCTCACTTTAAATATATAAGTCA-CTT-TT-------CTA-T--------AAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGATTGTAG-CAA-TACT-GCCATCTT---------ATTT---------A-AGGGAGACTCCTAAAAA--------CCCA-ATTTTAA---------CCTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_durus_LC203758 GATCATTATTAAAAGACTTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA-----TCTTACCCAAAC--TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCTTCTTCTTTTT-----------------TTATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAAAA------CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATGGCTTAGTGGATGTTGAGTGTTGCTGTCAT-TA-------GCTCACTTTAAATATATCAGTTA-CTTTT--------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT-----GTTTATAT---------A-AAAGGGACTTCTAAAAAAAA-----CCC--A-ATTAA---------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_erythronii_LC203755 GATCATTATTAAAAGAATTAGAGTGCACTTCATTGTGGC-TCGACC-CTTTT-----AAATAC-----CACCCAAAC--T--C-AAAA-CTTGGTTGCATGATTT-----A---TCATTGCAATTGAGTATAAGTAAC-TT-T-------AT-GTTACATTACCCC-CCCTTTCTT-----------------------------ATT-ATATA---CACAAGTTTAAAT---GAATGTAAAA--CC---CCCTT--AATTA-AAA-----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAA-T-ATTT-------ATTTATTT--TA---GTGGATGTTGAGTGTTGCTGTTAT-TA-------GCTCACTTTAAATATATAAG--ATCT-----------CAAAT--------AAGTTGGATTGACTTGGTGT--AATAAT---TTAT-T--TCACATCAAGGAAAGTAG-CAA-TACTTGCCATCTT----------TTTT-GT----------GAGACTACTAAA--C-------CCC--ATAT-AAT--------TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_japonicus_LC203759 GATCATTATTAAAAGAATTAGGGTGCACTTCATTGTGGCCT-GACTTC--------AAAATAC--TTTCACCC------TCCCAAAGA-CTTGGTTGCATGGTT---A--ACA-CCATTGCAATTGAGTAGACGTAAC-TTCTTTATTGAAT-GTTGCATTACCCCTCCCTTTTT------------------------ATT-TAATT-ACATA---CACAAGTTTAAAT---GAATGTAAAAAA--A--CCCTTT-AATTG-AAAA----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAA-TAATTTTTTCTCTAAA-ATTATTTACAAGTGGATGTTGAGTGTTGCTGTAAT-TA-------GCTCACTTTAAATATATAAGTCA-CT-CTT-------CTAGT--------AAGATGGATTGACTTGGTGTGTAATAATAACTTGTTC-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATTTT---------ATTTT-------GA-AGGGAGACTCCTAAAA---------CTT--ATAT-A-TTATTT---TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_japonicus_LC203760 GATCATTATTAAAAGAATTAGGGTGCACTTCATTGTGGCCT-GACTTC--------AAAATAC--TTTCACCC------TCCCAAAGA-CTTGGTTGCATGGTT---A--ACA-CCATTGCAATTGAGTAGACGTAAC-TTCTTTATTGAAT-GTTGCATTACCCCTCCCTTTTT------------------------ATT-TAATT-ACATA---CACAAGTTTAAAT---GAATGTAAAAAA-----CCCTTT-AATTG-AAAA----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAA-TAATTTTTTCTCTAAA-ATTATTTACAAGTGGATGTTGAGTGTTGCTGTAAT-TA-------GCTCACTTTAAATATATAAGTCA-CT-CTT-------CTAGT--------AAGATGGATTGACTTGGTGTGTAATAATAACTTGTTC-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATTTT---------ATTTT-------GA-AGGGAGACTCCTAAAA---------CTT--ATAT-A-TTATTT---TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_japonicus_LC203761 GATCATTATTAAAAGAATTAGGGTGCACTTCATTGTGGCCT-GACTTC--------AAAATAC--TTTCACCC------TCCCAAAGA-CTTGGTTGCATGGTT---A--ACA-CCATTGCAATTGAGTAGACGTAAC-TTCTTTATTGAAT-GTTGCATTACCCCTCCCTTTTT------------------------ATT-TAATT-ACATA---CACAAGTTTAAAT---GAATGTAAAAAA-----CCCTTT-AATTG-AAAA----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAA-TAATTTTTTCTCTAAA-ATTATTTACAAGTGGATGTTGAGTGTTGCTGTAAT-TA-------GCTCACTTTAAATATATAAGTCA-CT-CTT-------CTAGT--------AAGATGGATTGACTTGGTGTGTAATAATAACTTGTTC-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATTTT---------ATTTT-------GA-AGGGAGACTCCTAAAA---------CTT--ATAT-A-TTATTT---TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_japonicus_LC203762 GATCATTATTAAAAGAATTAGGGTGCACTTCATTGTGGCCT-GACTTC--------AAAATAC--TTTCACCC------TCCCAAAGA-CTTGGTTGCATGGTT---A--ACA-CCATTGCAATTGAGTAGACGTAAC-TTCTTTATTGAAT-GTTGCATTACCCCTCCCTTTTT------------------------ATT-TAATT-ACATA---CACAAGTTTAAAT---GAATGTAAAAAA-----CCCTTT-AATTA-AAAA----TAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCACAAAA-TAATTTTTTCTCTGAA-ATTATTTACAAGTGGATGTTGAGTGTTGCTGTAAT-TA-------GCTCACTTTAAATATATAAGTCA-CT-CTT-------CTAGT--------AAGATGGATTGACTTGGTGTGTAATAATAACTTGTTC-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATTTT---------ATTTT-------GA-AGGGAGACTCCTAAAA----------TT-----T-A-TTATTT---TTTTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_reichertii_AF511084 GATCATTATTAAAAGAATTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA------C-CACCC------TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGCAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCCTTTTCTTTTTTC----------------GATTATT-ATTAA---CACAAGTTTAAAT---GAATGTAAAA--CAA---CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATTGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCYGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATAGTTTAGTGGATGTTGAGTGTTGCTTTTGT-TA-------GCTCGCTTTAAATATATCAGTTA-CTTTTTT------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-GTCACATCAAGGAAAGTAG-CAA-TACTTGCCATCT-------CTAAAAA---------A-AAAGGGACTTCTAAAAAA-------CCC--A-ATTAATTATTAT--TATTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_scillarum_AF511085 GATCATTATTAAAAGAATTAGAGTGCACTTTATTGTGGC-TCGACCCCTTTTTT---AAA------C-CACCC------TAACTAAGA-CTTTTTTGCATGATTT-GA-AAGAATCATTGTGACTAAGTAGACGTAAC-TTCTTAATTGAAT-GTTGCATTACCCCCCC-TCCTTTTCTTTTTTT--------------TTGATT----ATTAA---CACAAGTTTAAAT---GAATGTAAAA--CAA---CCTTTAAATTAT-----ATATAACTTTTAACAATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATTGAATCTTTGAACGCATCTTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAACCCTCTCATTAAACCATTTTGTTCTTGAACAAG-ATAGTTTAGTGGATGTTGAGTGTTGCTTTTGT-TA-------GCTCGCTTTAAATATATCAGTTA-CTTTTT-------CAAAT--------GAGTTGGATTGACTTGGTGT--AATAAT--TTTAT-C-ATCACATCAAGGAAAGTAG-CAA-TACTTGCCATC--------TTTAAAA---------A-AAAGGGACTTCTAAAAACAAA----CCC--A-ATTAAT--------TATTAAGACCTCAAATCAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGA Uromyces_striatus_FJ468409 GATCATTATTTAAGCCAAATGAGTGCACTTTATTGTGGC-TC-AACATTT---------ATA-CATCTCACCACTAA---AACTT-G-TTTGTGTGGCAT--TTT-------TGTCATTGCACTCAGGTAGACGTAAC-AT-TT--TT-T-T-GTTACATTATCCCCTCCC-----AATTTTT-----------------TTTTTTTTTATAAA---CACAAGTT-GAATTAAGAATGTAAAAA-------CCTTTTTATTTTGAAA----TAACTTTTAACAATGGATCTCTTGGCTCTCATATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATTGAATCTTTGAACGCACCTTGCACCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAAATCTCTCATCAAATTAATT-------------------TTTGGTGGATGTTGAGTGCTGCTGTTATCTA-------GCTCACTTTAAATATATAAGTT--CTTTCT--------------TATGTT-TGTTGGATTGACTTGGTGT--AATATTTATTTT----ATCA--TCAAGGAAAGTAG-AAA-TACTTGCCAAC-------ATTTTTAATTT----------AAGGACTTCTAAAT-GA-------------ATTATTTTCTTACTTTTTAAGACCTCAAATCAGGTGGGACTACCTGCTGAACTTAAGCATATCAATAGGCAGAGGA ; END; BEGIN TREES; Title Uromyces_japonicus_phylogeny; ID 0159b5d18e4d18; LINK Taxa = Uromyces_japonicus_phylogeny; TRANSLATE [0] 1 Puccinia_allii_LC203757, [1] 2 Puccinia_allii_AF511077, [2] 3 Puccinia_allii_KU296877, [3] 4 Puccinia_allii_KU296882, [4] 5 Puccinia_allii_KU296883, [5] 6 Puccinia_allii_LC203756, [6] 7 Puccinia_allii_KU296869, [7] 8 Puccinia_andropogonis_EF583818, [8] 9 Puccinia_asparagi_AY217137, [9] 10 Puccinia_hordei_AY874150, [10] 11 Puccinia_mixta_KU296895, [11] 12 Puccinia_obscura_AF468042, [12] 13 Puccinia_porri_AF511073, [13] 14 Puccinia_porri_KU296909, [14] 15 Puccinia_striiformis_EU014048, [15] 16 Uromyces_durus_LC203758, [16] 17 Uromyces_erythronii_LC203755, [17] 18 Uromyces_japonicus_LC203759, [18] 19 Uromyces_japonicus_LC203760, [19] 20 Uromyces_japonicus_LC203761, [20] 21 Uromyces_japonicus_LC203762, [21] 22 Uromyces_reichertii_AF511084, [22] 23 Uromyces_scillarum_AF511085, [23] 24 Uromyces_striatus_FJ468409; TREE 170119.aln__tree = ((((((((((2:0.0,4:0.001543675648906663)53:0.00001984631057552646,11)35:0.00002650546018069657,1)33:0.00021469022505519547,16)29:0.0002512123690027089,((6:0.0,5:0.0)61:0.00001785224336976971,3:0.0015229810253342864)61:0.0011593495288913843)37:0.0005147262487661536,7:0.0007674146085291855)87:0.004145851633914341,(14:0.00004868200978082153,13)100:0.006546017572627521)88:0.005000094260027449,((23:0.0016400780968522342,22:0.009461311686811183)97:0.010891446622310183,10:0.00431890100336813)87:0.004594684303635212)100:0.027926146338253643,((((((20:0.0,19:0.0)57:0.00003846723625935272,18)57:0.0014173479677878145,21:0.0017775510815976905)100:0.03846884155534731,15:0.01846505032608118)70:0.00908609073504129,17:0.00915571518211893)42:0.002651453766486539,(9:0.028083499560676323,8:0.025217888202596232)99:0.015243870014377395)100:0.021485987371191062)100:0.0337046558652125,(24:0.03849776386329061,12:0.04564462443157233)100:0.0337046558652125):0.0; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 764; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 764; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 764; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1484816410083; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 3178027516727926548; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3272996621500679810; mqVersion 320; checksumv 0 3 3151322665 null getNumChars 764 numChars 764 getNumTaxa 24 numTaxa 24 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 393362.0 sumSquares -3.22818021289917E19 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1 errorReportedDuringRun; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1582 748; setLocation 145 91; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #3178027516727926548 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #3178027516727926548; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1482 676; setLocation 145 91; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; 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.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #3178027516727926548 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 0159b5d18e4d18; toggleUseWeights off; endTell; setAssignedID 3111.1484814140424.7601338842572898010; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1482 676; setLocation 145 91; 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 off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3272996621500679810 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1482 676; setLocation 145 91; 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.AlterData.AlterData; tell It; toggleBySubmenus off; 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;