#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 May 18, 2024; 3:47 GMT

TreeBASE (cc) 1994-2008

Study reference:
Davis J., Simmons M., Stevenson D., & Wendel J. 1998. Data decisiveness, data quality,
and incongruence in phylogenetic analysis: and example from the monocotyledons
using mitochondrial atpA sequences. Systematic Biology, 47(2): 282-310.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S398]

[ The following blocks are input data for analysis step 469 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep469;
        DIMENSIONS NTAX=20;
        TAXLABELS
            Acorus
            Alstroemeria
            Anigozanthos
            Canna
            Catopsis
            Curculigo
            Eriocaulon
            Flagellaria
            Gymnostachys
            Nypa
            Oryza
            Piper
            Saruma
            Smilax
            Symplocarpus
            Tacca
            Trillium
            Vellozia
            Veratrum
            Xanthorrhoea
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2090]

	TITLE rbcL;
	LINK TAXA = TaxaForAnalysisStep469;
	DIMENSIONS NCHAR=242;
	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  ]
[                         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .  ]
Acorus           TCCATGAATTCAACC?AGTGTCGCCCCCGCCCGTTGGAATATCCGTGCCCTGGCTTCCGTCCACGCT?GGAGGTTCCATGCGGCCAAACTACGGCGAGTCTATAGGAATAATGTGTGCCAAGCAGTTTCGTATGCGATTACCCCTTGGCTCG?TAGCCAAGGATAGACTTACAAGTTTACTATTGCACCTCGCGGTCGCTTACAATATCGATGGACACCATTGT??????????????????
Alstroemeria     CCCCCGAACTTAGCCAAGTGTTGTT?CTGACTATTGGAATATCCGTTTCCTGGCGTCCGTCCACGCCTAAAGGCTCCGCACAGCCGGAATACGACGCATTCACTGGAGCAGCGGGTATGTATTAGTTTCAACGGCGTATCCCCTCTAGTTCATCAGCTAAGGATGGATTTTCAAGTTTACTACTGCGATTCGCAGTCGCTTAT?GTATCAGTAGGTAAGATAGTCCCGAGACGCGCGAAG?G
Anigozanthos     CTCGTGAGCTTAGCTAAGA?TTGTTATCGCCC?TTGGAATGTCCGTTCCCTGGTATCATTCAATG?CCAAGGGCTCCATACAGTCGGAATACAACAAACTCAAAGGAGTAACGCGTTTGTATCAATCTCGTTGGCGCATTCCCCTCAGTTCATTATCTAAGGGCGGATTTATAAGCTTACTATCGTGGTTTGCAACTGTCTACAAGATCAGTGGATA?GACGCCT?TGAAATACCCAGAGCA
Canna            TTCC??AACTCAACCAAGTGTTGTT?TCGCGCGTTGGTATATCCGTTCCTCGGCGTCCGTCTATGTCCGAGGGTTCCATATAACCACAATACAACGAATTCAATTAGATAACGTGTTCGTATCAATTTCGTTTGCGCATTCCCCCTACTCCATTAGCTAAG?GTGGATTTATAAGCT?ACTATA?CGATTTGCAGCCGTCTACA?TCTAGGTGGA?AAGATAGCCT????????????????
Catopsis         ?TCGCGAACTCAGCTAAGTGATTTTACCACCCGTCGGAATATCCATTCCCCGGCGTCATTCAACGTTCAAGGGTTTCATACAGCCAGAACGCAACGAATGCAAAGGGGTAACATGTGCATATCAGTTTCGTTGGCGCATCCTCCTCAGTTCATTAGCTAAGGATGGGTTTTCTAGTCTACTATAATGATTT?CAACCGTTTGCAATATCGGTGAATACGATAGCCCTGAAACCTCCGAAGCA
Curculigo        TTCCCGAACTTAGCTGAGAGTTGTTACCGGCCATTGGAACATCCGTTCCCCGGCGTCCGTCTAAGTTCAAAGGTTCCGTACAACCAGAATACGACGAATTCAAAGGAGTAACGAGTGCGCAGCAGTTTCATCTCCGATTCCCCCTCAGTTCATTGGGCAAGGATGGGTTTACAAGCTTACTATTGCGATTCACAGCCGCTTACAACATAGACAGATAAACTAGCCTAGAGACGCAGAGAGCA
Eriocaulon       CTCACGAGTCC?TGTAGCTGTCTTCATAGCCTGTTGAAATACTTGTTCTTTAATACTCGTCAATATCTAAGGATTCCATATAGCTA?AACACAACAAATTC?AAGGGATAGCGTGTCTGTATCAGTTTTGATGGTACAGCCTCCTCGATTCATGAGCCAGGGATGGGTTCTC?GCC?TATC?CAACGGTCTGCAG?CGTTTGCAGTACCAGTGAACAAGATTGC??????????????????
Flagellaria      TTCGCGAACTGAACTGAGTGTCTTTATCGCCTGTTGGAATATTCATTCCCCGGCGTCATTCAACCTTCAAGGGTTCTATACAGCCAGAATACAACGAATTCGCAGAGGTAGCGTA?CCACAGCAGTTTCGTTGGTGCATCCTCCC?AGTCCGATGGCTAAGGATGGATTTTTTAGC?TACTGTCGGGATTTGCAACCGTTC?CAATATCAGTGAGTAAGATTGCTCAGAACCGCGCGACGAA
Gymnostachys     CCCCTGGACTCAACTAGGTATTGTCACCGGCCGTTGAAACATCCGTGCTTCGGCTTTCGTCCACGCTCAGAAGTTCCAGACGACCAGACCACGGCGAATCCATAGGGATAACGTATGTGTGTTAGCCTTGTAGGTGTATACCCCTCGGTTCATTAGCTAAATGTGGGTTTACAAGTTTAATATCGCGATTCGTGGCCGCTTACAACATCGGCGGATAAGATAGCTCTGAGACAC????????
Nypa             CTCCCGAACTCAGCTGAGAGTTGTTACCAACCGTCGGAATATCCGTTCCCCGGCGCCCTTCCACATTCAAGGGTTTCATACAGCCGGAACACGACGAATTCAAAGGGGTAACGTGTGCATATCAGTTTCATTGGCGCATCTCCCTCAGTTCATTAGG?AGGGATGGGTTTTCAAGCCTACTATAACGATTCGCAGCTGTCTACAACATCGGTGGATAAGATAGCCTCGAGACCC????????
Oryza            TTTGCGAGCTGGGCCAAGTATTTTTCTCGCCCGTTGGTATGTCCGCTCCCCGGCGTCC?TCAATGTTTAAGGACTTTATATAATTAAGACACAACAAATGC?AATAGCTGGCGGACTTGTAT?GATTTTGTCGGTGCATCCCCTC?AGTCTATGAGCTAAAGACAGATCTTTTGCCCTGACATAAGGAT?TGCAATTATTTATTATACCGGT?AGTAAGA?TGCTCAAAACCGCGCGAAACA
Piper            TCCATGAGCCCAGCTGAGTGTTGCCACCGCCCGCTGGAACGTCCATATTCCGATGTTATATCGCGTCCAGAGGTCCCATACCGCCGGACCACGGCGCACTCAAAGAGATAACGTACCCGTATCGGCTCCGTAGGCGCATACCCCTCGGCTCGTCAGCTCAGGAT?CGCTTTC?AGCTAACTGTCGCGATCTGCGGCCACTTACAA?CTCGGTGGATGAGATAGC??????????????????
Saruma           TCCCTGAACTCAGCTGAGTGTTGCCACCGCCTGCTGGATCATCTGTACCCCGGCATTCGTCCAT?CTTAGAGGTTCCATG?CGCCAGACCACGGTGCATTCAAATAGACAGCGTACCCGTATCAGTTTCGTAGGCGCAT?TCCCTTGACCTGTTAGCTCAGGA?ACGCTTTCAAGCTAACTATCGTGACTCGCGGCCGCTTACAATATAGGTGGGTAAGATGCCT?TAAGACATAGAGC?TG
Smilax           TCCCTGAATTCAGCTAAG?G?TGTTACAGAGCGTTGGAATACCCGTTCCCCAGTGTTATTCCACACTCAAAGGTTCCACACAGCCAGA?CACAACGAATGCACTGGGGTAACGTGTGCGCATTAGTTTCGT?GCTACATATCCCTCAGTCCATCAGCTAAGGATGGACCTTCAAG?TTACTATTGCACCCTACAGCCGCCCACAGTATCAGCG?????????????????????????????
Symplocarpus     TCCCTGGACTCAACTAA?TATTTTCACCGGCCGTTAGATCGTCCGTGCTTCGGCTTTCGTCAACACCCAGAGGTTCCAGATGACCAGA?CACGGCGAATTCAAAGGGATAATGTATCTGTGTCAGCTCCGTAGGTGCATACCCCTCGGTCCATTATCTAAGTATGGGTTTACAAGTTTACTATCGCGATTCGTGGCCGCTTACAACATCGGCGGATAACATAGC??????????????????
Tacca            TCTCCGAACTCGGCCAA?TATTGTTACCAAGTGCT?G?ATATCCATTCCCCGACGTTATTCCACGTTCAAGGGTCCCATGCAGCCACAACA?GAT?AGTGTGCAGGAGCGACGTGTATGTAT?AGCTTCGTATGCGCATCTT?CTCAGTTCATTAGCTAAGGGTGGGCTTACAAGCTTACTGTAACGATTCGCAGTCGCTTGCAATATCGGTGGATAAGATAGCTCTGAGACACACAACACA
Trillium         CCCCCAAACTCAGGTAGCTGATGTTACCGAGCGCTGGAATATTCGTGCCCCAGCGTTCGTCAACGCTTGAAGGCTCCA?ATAGCCAAGACATGACGAATTCAAAGGGGTAGCGCGTGCGTATTAGTTTCGTTGGCGCATCCCCTTCAGTTCATTAGCTAGGGATGGACTTTCAAGTTTGCTATCGCGATTCGCAGCCGCCTATAATATCAGTAGATAAGATTGCCCTGCG????????????
Vellozia         ??CCCGAACTCAGCTAAGAGTTGTTACTGAGCGTTGGAATATTCACTCCCCAGCGTT?TATCGAGTTTGAAGGTTTTATATAGCCGGAATACAACGAACTCAAAGAGATAACATATCCGTATCAGCTTCG?TGGCGCATTCCACCCAGTCCATTATCTCAAGATGGACTTTCAAGTTTACTATCATGATTCGCAGCCGCTTACTAG?TCAATAGATAAAATAGCCCTGAGATACACAAAGTA
Veratrum         CCCCCAAACTTAACTAAC?GTT?TTACTGAGCGTTAGAATATCCGTTCCCCGACGTTATTCCACGCCTAAAAGTTCCACACAGCCACAACATGACGAATGCAAAGGAATAACGCGTGCCAATCAGTTCCGTTGCCGCAGCCCACCCACTCCATTAGCTAGG?ATGGACTCTCAAGTTTACTATCACAATTCGCAGCCGCCTGCAATATCAGTGGATGAGACTGCCCTGCG????????????
Xanthorrhoea     TTC?CGAACTCATCTAAGTGTT?CCACTGGCCGTTGAAATATCCGTTCCCCGGCATCCTTCCA?CCCCAAAGGCTCCATACAACCAAAACGCGACGAATGTAAAGGACTAACGAATCCGTATCAGTTTCGTTGGTGCATCCCCCTCAGTTCGATAGCCAAGGATGGATTTTCAAGCTTATTATA?CGATTCACAACCGCTTACAAC?TCGATGGATAAGCCTGCCCTGAACCACACGAAGAA
;
END;

[ The following blocks are output data for analysis step 469 ]
BEGIN TREES;
      TITLE Tb5249;
      LINK TAXA = TaxaForAnalysisStep469;
      TREE Fig._3a = [&R] (Piper,Saruma,(Acorus,((Gymnostachys,Symplocarpus),(Tacca,((Vellozia,((Alstroemeria,Smilax),(Trillium,Veratrum))),((Curculigo,Xanthorrhoea),(Nypa,((Anigozanthos,Canna),(Catopsis,(Flagellaria,(Eriocaulon,Oryza)))))))))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3354]


END;