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#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;
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