#NEXUS
BEGIN TAXA;
    TITLE firstt;
    DIMENSIONS NTax = 6;
    TAXLABELS P._fimbriata P._robusta P._americana P._myriophylla P._polygama P._macrophylla;
    blockid bogus;
END;
BEGIN TAXA;
    TITLE second;
    DIMENSIONS NTax = 6;
    TAXLABELS P._fimbriata X._robusta P._americana N._myriophylla P._polygama P._macrophylla;
    blockid bogus2;
END;
BEGIN CHARACTERS;
    TITLE firstchars;
    LINK TAXA = firstt;
    DIMENSIONS NChar=45;
    FORMAT Datatype=DNA  Gap=-;
Matrix
P._fimbriata       RCCTCGGCTTAACGAACCTCGGCTTAACGAACCTCGGCTTAACGA
P._robusta         (AC)CCTCGGCTTAACCAACCTCGGCTTAACGAACCTCGGCTTAACGA
P._americana       RCGTCGCTTTCA---ACGTCGCTTTCACCAACGTCGCTTTCACCA
P._myriophylla     ACGTCGCTTTCA---ACGTCGCTTTCACCAACGTC?CTTTCACCA
P._polygama        ACGTCGCTCTCACCAACGTCGCTTTCACCAACGTC?CTTTCACCA
P._macrophylla     ACGTCGCTCTCACCAACGTCGCTTTCACCAACGTCGCTTTCACCA
;
END;
BEGIN CHARACTERS;
    TITLE second_chars;
    LINK TAXA = second;
    DIMENSIONS NChar=45;
    FORMAT Datatype=RNA  Gap=-;
Matrix
P._fimbriata       YRCUCGGCUUAACGAACCUCGGCUUAACGAACCUCGGCUUAACGA
X._robusta         NCCUCGGCUUAACCAACCUCGGCUUAACGAACCUCGGCUUAACGA
P._americana       ACGUCGCUUUCA---ACGUCGCUUUCACCAACGUCGCUUUCACCA
N._myriophylla     ACGUCGCUUUCA---ACGUCGCUUUCACCAACGUC?CUUUCACCA
P._polygama        ACGUCGCUCUCACCAACGUCGCUUUCACCAACGUC?CUUUCACCA
P._macrophylla     ACGUCGCUCUCACCAACGUCGCUUUCACCAACGUCGCUUUCACCA
;
END;
BEGIN TREES;
    TITLE first_trees;
    LINK TAXA = second;
    TRANSLATE
        1 P._fimbriata,
        2 X._robusta,
        3 P._americana,
        4 N._myriophylla,
        5 P._polygama,
        6 P._macrophylla;
    TREE one = [&U](1,2,(3,4)5,6);
END;
BEGIN TREES;
    TITLE second_trees;
    LINK TAXA = firstt;
    TRANSLATE
        1 P._fimbriata,
        2 P._robusta,
        3 P._americana,
        4 P._myriophylla,
        5 P._polygama,
        6 P._macrophylla;
    TREE one = [&U](1,2,(3,4));
END;
BEGIN SETS;
    LINK CHARACTERS = firstchars;
    CHARSET p = 2-7 9-12 14-24 \ 2 44 45;
    CHARSET r = 2-12 15-24 \ 3 44 45;
END;
BEGIN SETS;
    LINK TAXA = second;
    TAXSET p = 1-5 \ 2;
END;
BEGIN SETS;
    TITLE mixedupassump;
    LINK TAXA = firstt CHARACTERS = second_chars;
    TAXSET o = 1 2;
    CHARSET o = 1-5 7-11 \ 2 12-24 \ 2 30-45 \ 5;
END;
BEGIN SETS;
    TITLE explicit;
    LINK TAXA = firstt CHARACTERS = second_chars;
    TAXSET o = 1 2;
    CHARSET oe = 1-5 7-11 \ 2 12-24 \ 2 30-45 \ 5;
END;
BEGIN SETS;
    TITLE explicit2;
    LINK TAXA = second CHARACTERS = firstchars;
    TAXSET pe = 1-3 5;
    CHARSET pe = 2-7 9-12 14-24 \ 2 44 45;
END;
