#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 July 12, 2025; 11:07 GMT TreeBASE (cc) 1994-2008 Study reference: Farmer S., & Schilling E. 2002. Phylogenetic analyses of Trilliaceae based on morphological and molecular data. Systematic Botany, 27(4): 674-692. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S953] [ The following blocks are input data for analysis step 1611 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1611; DIMENSIONS NTAX=26; TAXLABELS Daiswa_fargesii Daiswa_polyphylla Daiswa_thibetica Daiswa_violacea Kinugasa_japonica Paris_incompleta Paris_tetraphylla Paris_verticillata Trillium_camschatcense Trillium_chloropetalum Trillium_decipiens Trillium_discolor Trillium_erectum Trillium_govanianum Trillium_grandiflorum Trillium_lancifolium Trillium_maculatum Trillium_ovatum Trillium_petiolatum Trillium_pusillum Trillium_recurvatum Trillium_reliquum Trillium_rivale Trillium_rugelii Trillium_sessile Trillium_undulatum ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M471] TITLE ITS.nex; LINK TAXA = TaxaForAnalysisStep1611; DIMENSIONS NCHAR=648; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Daiswa_fargesii TCGAGATAATAAATATGGTCGGAAGATTGTGAACTCGTGAAGGAA-TGAT-GATTATGGTGGAGGGTTCGTCCCGAAGCCAA-AGCCCC-TACAACCCTTGAGTCGAAAGGGAGCCATAGGCGTGGC---ACGACGCATGTGTGGGT--GGGGCGCTAACAAAACTCGGCGCAACAAGCGTCAAGGAACGAGTATGTGAATACGA-CCCATTGTCATTAGCC-GATCAGTGGTCT---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGATCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGATGTCATTCGGCAAAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACGCCTGTGGGTCGAAAGTTTGGCACGGATGTGGAGATTGGCCTCCCGTGTCC-TTGTGCGCGCGGTAGGTTGAAGAGT--GGGAT--GCCAATGGAGACGGACACGGCGAGTGGTGGATATGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGGGG------CCC---TT-GTGACACCCAGTATGGTTGCGC--TGTAT Daiswa_polyphylla TCGAGATACGAAATGTGGTCGGAAGATTGTGAACTTGTGAACGAA-TGAT-GATTATGGTGGAAGGTTCGTCCCGAAGCCAA-AGCCCC-TACACCCCTTGAGTCGAAAGGGAGCCATAGGCGTGGC---ACGGCGCATGTGTGGGT--GGGGCGCTAACAAAACTCGGCGCAACAAGCGTCAAGGAATGAGTATGTGAATACGG-CCCACTGTCATTAGA-TGATCAGTGGTCT---TATGTTTCACAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGTCATTCGGCAAAGGGCACGCCTGCCTGGGCGTCATGTCTTGCGTCGCTCGGTGCCAACTATGCCCGTGGGTCGAAAGTTTGGCACGGATGTGGAGATTGGCCTCTCGTGTCC-TTGTGCGCGCGGTAGGCTAAAGAGT--GGGAT--GCCAACGTAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGGGG-----CCCC---TT-ATGACACCCAACATGGTTGCGC--TGTAC Daiswa_thibetica TCGAGATACTAAATGTGGTCGGAAGATTGTGAACTCGTGAACGAA-TGAT-GATTATGGTGGAGGGTTCGTCCCGAAGCCAA-AGCCCT-TACACCCCTTGAGTCGAAAGGGAGCCATAGGCGTGGC---ACGGCGTATGTGTGGGT--GGGGTGCTAACAAAACTCGGCGCAACAAGCGTCAAGGAACGAGTATGTGAATGCGG-CCCACTGTCATT-GGCTGATCAGTGGTCT---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGTCATTCGGCAAAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACTCCTGTTGGTCGAAAGTTTGGCATGGATGCGGAGATTGGCCTCTCGTGTCC-TTGTGCACACGGTAGGTTGAAGAGT--GGGAT--GCCAACGGAGACGGACACGGCGAGTGGTGGATGTGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTTGGGGGA-----CCC---TT-GTGACACCCAGCATGGTTGCGC--TGTAT Daiswa_violacea TCGAGATACTAAATGTGGTCGGAAGATTGTGAACTTGTGAACGAA-TGAC-AATTATGGTGGAGGGTTCGTCCCGAAGCCAA-AGCCCC-TACACCCATTGAGTCGAAAGGGAGCCATAGGCGTGGC---ACGGCGCATGTGTGGGT--TGGGCGCTAACAAAACTCGGCGCAACAAGCGTCAAGGAACGAGTATGTGAATGCGG-CC-ACTGTCATTAGC-TGATGAGTGGTCG---TATGTTTCACAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAAAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACGCCCGTGGGTCGAAAGTGTGGCACTGATGTGGAGATTGGCCTCTCGTGTCC-TTGTACGCGCGGTAGGCTGAAGAGT--GGGAT--GCCAACGGAGACGGACACGATGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG-----CCCC---TT-ATGACACCCAACATGGTTGCGT--TGTAT Kinugasa_japonica TCGAGATACAAAATGTGGTCGGAAGACTGTGAACTCGTGAACAAA-TGAA-AATTATGGTGGAGGGTTCATCCTGAAGCCAA-TGCCTC-TACCCT--TTGAGTCGAAAGCGAGCCATAAGCGTGGC---ACGGCGCATGTGTGGGT--TGGGCGCTAACAAAACCCGACGCAACACGCGTCAAGGAATGAGTATGTGAATGCGG-CCCACTGTCTTT-GGTCGATGCGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGACAGAGGGCACGCCTGCTTGGGCGTCACGTCTTGTATCGCTCGGTGCCAACTGCGATAGTGGGTCGAAAGTGTGGCATGGATGTGGAGATTGGCCTCCCGTGCCT-TTGTGCGTGCGGTGGGTTGAAGGGT--GAGAT--GCCAACGGAGACGGACACGGCGAGTGGTGGAAGCGAGCCGGACGTCGTGGTCTCGTGCTCTAAAGGCTCGGAGT-----CCCC---TT-GTGACACCCAATAGGGTTACGC--TGCAC Paris_incompleta TCGAGATATGAAATGTAGCTGGAAGACTGTGAACTCGTGAATGAA-TGAT-GATTTTGGTGGAGGGTCCGTCCTGAAGCCAA-TACCCC-TGCCCT--TTGAGTCGAAAGCGAGCCATAGGCATGGC---ACGACGTATGTGTGGGTGGGGGGCGCTAACAAAATCCGACGCAGCATGCGTCAAGGAACGAGTACGTGAATGAGG-CCTACT-TCATT-GGTTGATGAGTGGTCC---TATGTTTCGTAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCATCGCTCGGTGCCAACTACGCTCGTGGGTCGAAAGTATGGCACTGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGTGCAGTGGGTTGAAGAGT--GGGATATGCCAACGGAGACGGACACGACGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCATCCTCTAAAGGCTCGGGGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGC--TGCAA Paris_tetraphylla TCGAGATATGAAATATGGCCGGAAGACCATGAACTCGTGAACGAA-TGAT-GATTTTGGTGGAGGGTCCGTCCTGAAGCCAA-TGCCCC-TGCCTC--TTGAGTCGAAAGCGAGCCATAGGCATGGC---ACGGCGCATGTGTGGGTGGGGGGTGCTAACAAAACCCGATGCAGCACGCGTCAAGGAACTAGTACGTGAATGAGG-CCCACTGTCATT-GGTTGATTAGTGGTCC---TATGTTTCGTAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACGCTCGTGGGTCGAAAGTTTGGCACGGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGCACGGTAGGTTGAAGCGTGTGGGAT--GCCAATGGAGACGGACACGACGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCATCCTCTAAAGGCTCGGGAG-----CCCC---TT-GTGACACCCAGTAGGGCTGCGC--TGCAA Paris_verticillata TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGAT-GATTTTGGTGGAGGGTCCGTCCTGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCATGGC---ACGGCGCATGTGTGGGT-GGGGGCGCTAACAAAACCCGACGCAACACGCGTCAAGGAACGAGTACGTGAATGAGG-CCCACCGTCATT-GGTTGATGAGTGGTCC---TATGTTTCGTAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACGCCCGTGGGTCAAAAGTGTGGCACGGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCAACGGAGACGGACACGACGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGGGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGC--TGCAA Trillium_camschatcense TCGAGATACGAAATGTGGTCGGAAGACTGTGAACTCGTGAACGAAATAATCGATTTTGGTGGAGGGTTCGTCCCGAAGCCAA-TGCCTC-TGCCCC--TTGAGTCGAAAGCGGGCCATAGGCGTGGCGCGACG-CAAGTAT--GGGTAAGGGGCGCTAACAAAACCCGGCGCAGCACGCGTCAAGGAACGAGTACGTGAA-GCGG-CCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCTCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCTGAGGGCACGCCTGCTTGGGCGTCACGCCTTGCGTCGCTCGGTGCCAATTGCGCTCGTGGGTCGAAAGGTTGGCACGGATGCGGAGATTGGCCTCCCGTGCCCCTTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGGG-----CCC---TT-GGGACACCCAGTAGGGTTGCGC--TGAAC Trillium_chloropetalum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_decipiens TCGAGATATGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGCCGAAATCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGTTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCGGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTCGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCCC-TGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GTCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTGAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_discolor TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAATCGAGCCATAGG{CT}GTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCGGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTCGAAAGGATGGCACGGATGCGGAGACTGACCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--TGGAT--GTCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTGAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_erectum TCGAGATACGAAATGTGGTGGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTCGTCTCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTTGAAAGCGGGCCATAGGCGTGGCGCGACG-CACGTGT--GGGT-GGGGGCGCTAACAAAACCCGGCGCAGCACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGATCAGTGGTCC---TATGTTTCTCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCTGAGGGCACGCCTGCTTGGGCGTCACGCCTTGCGTCGCTCGGTGCCAACTGCGCTCGTGGTTCGAAAGTTTGGCACGGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGGG-----CCC---TT-GTGACACCCAGTATGGTTGCGC--TGAAC Trillium_govanianum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TG-TCGATTCCGGTGGAGGGTTCGTCCCGAAGCCAA-TGCCCC-TTCCCC--TTGAGTCGAAAGCGGGCCATAGGCGTGGCGCGGCG-CAGGTGT--GGGT-GGGGGCGCTAACAAAACCCGGCGCAGCACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGATGAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTCGAAAGTGTGGCACGGATGCGGAGACTGGCCTCCCGTGCCC-TTGGGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCAACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_grandiflorum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGACCGATTTCGGTGGAGGGTTCGTCCCGAAGCTAA-TGCCCC-TGTCCC--TTGTGTCGAAAGCGGGCCATAGGCGTGGCGCGACG-CACGTGT--GGGT-GGGGGCGCCAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGATCAGTGGGCT---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTACGCCCGTGGGTCGAAATTTTGGCACGGATGCGGAGACTGACCCCCCGAGCCC-TTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGGCGGACACGGCGAGTGGTGGATGAGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGGA-----CCC---TT-GTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_lancifolium TCGAGATACGAAAT{AG}TGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GG{AC}TGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_maculatum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGC{AG}CGGCG-CA{CG}GTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTT{AG}CGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_ovatum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGACCGATTCTGGTGGAGGGTTCATCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAATCGAAAGTGGGCCATAGGTGTGGCGCGGTG-CATGTGT--GGGT-GGGGGCGCTAACAAAACTCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATTTGGTTGAGCATTGGTCC---TATGTTTTGCATAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCACATGTGGGTCGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGACGGACGCGGCGAGTGGTGGATGCGAGCCGGATGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGT--TGCAC Trillium_petiolatum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTA{GT}TCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_pusillum TCGAGATACGAAATGTGGCCGGAAGACCGTGAACTCGTGAATGAA-TGACCGATTCTGGTGGAGGGTTCGTCCTGAAGCCAAATGCCCCCTGCCCC--TTGGGTCGTAAGCGGGCCATAGGCGTGGCGCGACG-CACGTGT--GGGT-GGGGGCACTAACAAAACTCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGTGCAGTGGTCC---TATATTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGCCTTGCGTCGCTCGGTGCCAACTACGCCCATGGGTCGAAATGTTGGCACGGATGCGGAGACTGGCCCCCCGTACCC-TTATGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATATGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGCGCTGAAC Trillium_recurvatum TCGAGATACGAAAT{AG}TGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_reliquum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAATCGAGCCATAGGCGTGGCGCGGCG-CACGTGT--GGAC-GGGGGCGCTAACAAAACCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCGGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTCGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCCC-TGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GTCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTGAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_rivale TCGAGATGCGAAATATGACCGGAAGACTGTGAACTCGTTAACGAA-TG-TCGATTCTGGTGGAGGGTTCGTCCTGAAGCCAA-TGCCCC-TGCCCC--TTGAGCCGAAAGCGGGCCATGGGCATCGTGCGGTG-CATGTGT--TGGT--GGGGCGCTAACAAAATTCGACGCAGCATGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACCGTCATT-GCCTGACACGTGGTGGTGGTATGTTTCGCAGAGTAATTTTATGACTCCCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGACAGAGGGCACGTCTGCCTGGGCGTCACGTCCTGCGTCGCTCAGTGCCAATTGCGCTCGTGG-----AAGTGTTGCATGGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGCG--GTGGGTTGAAGAGT--GGGAT--GCCAGCGGAGACGGACATGGCGAGTGGTGGATACGAGCCGGACGTCGTGGTCTTCTCCTCTAATGGCTCGGAGATAACT-CCC----AAGAA----------GGGTTGCGC--TGCAC Trillium_rugelii TCGAGATACGAAATGTGGTGGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTCGTCTCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTTGAAAGCGGGCCATAGGCGTGGCGCGACG-CACGTGT--GGGT-GGGGGCGCTAACAAAACCCGGCGCAGCACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGATCAGTGGTCC---TATGTTTCTCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCTGAGGGCACGCCTGCTTGGGCGTCACGCCTTGCGTCGCTCGGTGCCAACTGCGCTCGTGGTTCGAAAGTTTGGCACGGATGCGGAGATTGGCCTCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGAGT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGGG-----CCC---TT-GTGACACCCAGTATGGTTGCGC--TGAAC Trillium_sessile TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGATCGATTCTGGTGGAGGGTTTGTCCCGAAGCCAA-TGCCCC-TGCCCC--TTGAGTCGAAAGCGAGCCATAGGCGTGGCGCGGCG-CAGGTGT--GGAC-GGGGGCGCTAACAAATCCCGGCGCAACACGCGTCAAGGAACGAGTACGTGAATGCGGGCCCACTGTCATT-GGCTGAGCAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTGGAAAGGTTGGCACGGATGCGGAGACTGGCCCCCTGTGCCC-TTGTGCGCGCGGTGGGTTGAAGATT--GGGAT--GCCGACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGTCCTCTAAAGGCTCGGAGG------CCC---TTTGTGACACCCAGTAGGGTTGCGC--TGCAC Trillium_undulatum TCGAGATACGAAATGTGGCCGGAAGACTGTGAACTCGTGAACGAA-TGA-CGATTCCGGTGGAGGGTTCATCCTGAAGCCAA-CGCCCC-TGCCCC--TTGAGTCGAAAGCGGGCCATAGGCGTGGCGCGGCG-CAGGTGT--GGGC-GGGGGCGCTAACAAAACCCGGCGCAGCACGCGTCAAGGAACGAGTACGTGAATGCGG-CCCACTGTCATT-GGCTGATGAGTGGTCC---TATGTTTCGCAGAGTAATTTTATGACTCTCGGCAACGGATATCTTGGCTCCCGTATCGATGAAGAACGTAGCGAAATGCGATACTTGATGTGAATTGCAGAATCCCGTGAATCATCGAGTTTTTGAACGCAAGTTGCGCCCGATGCCATTCGGCAGAGGGCACGCCTGCCTGGGCGTCACGTCTTGCGTCGCTCGGTGCCAACTGCGCCCGTGGGTCGAAAGTGTGGCACGGATGCGGAGACTGGCCTCCTGTGCCC-TTGGGCGCGCGGTGGGTTGAAGAGT--GGGCT--GCCAACGGAGACGGACACGGCGAGTGGTGGATGCGAGCCGGACGTCGTGGTCTCGCCCTCTAAAGGCTCGGAGG-----CCCC---TT-GTGACACCCAGTAGGGTTGCGC--TGCAC ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = ITS.nex) = N: 1-648; CODONPOSSET CodonPositions (CHARACTERS = ITS.nex) = N: 1-648; END; [ The following blocks are output data for analysis step 1611 ] BEGIN TREES; TITLE Tb6387; LINK TAXA = TaxaForAnalysisStep1611; TREE Fig._1d = [&R] (Trillium_rivale,((((Daiswa_fargesii,Daiswa_polyphylla,Daiswa_thibetica,Daiswa_violacea)Daiswa,Kinugasa_japonica),((Paris_incompleta,Paris_tetraphylla),Paris_verticillata)Paris)Paris_s.l.,(((((Trillium_chloropetalum,Trillium_lancifolium,Trillium_maculatum,Trillium_petiolatum,Trillium_recurvatum,Trillium_sessile),((Trillium_decipiens,Trillium_reliquum),Trillium_discolor))Trillium_subg._Phyllantherum,((Trillium_grandiflorum,Trillium_pusillum),Trillium_ovatum)Grandiflorum_Group),(Trillium_camschatcense,(Trillium_erectum,Trillium_rugelii))Erectum_Group),(Trillium_govanianum,Trillium_undulatum))Trillium_plus_Trillidium)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr867] END;