#nexus
begin taxa;
  dimensions ntax=6;
  title firstt;
  taxlabels
	P._fimbriata
	'P. robusta'
	'P. americana'
	'P. myriophylla'
	'P. polygama'
	'P. macrophylla'
  ;
  blockid bogus;
end;

begin taxa;
  dimensions ntax=6;
  title second;
  taxlabels
	'P. fimbriata'
	'X. robusta'
	'P. americana'
	'N. myriophylla'
	'P. polygama'
	'P. macrophylla'
  ;
  blockid bogus2;
end;

begin characters;
	LINK TAXA= firstt;
  dimensions nchar=45;
  format datatype=dna missing=? gap=-;
  title firstchars;
  matrix
	P._fimbriata    {a, G}cctcggcttaacgaacctcggcttaacgaacctcggcttaacga
	P._robusta      (a, , C)cctcggcttaaccaacctcggcttaacgaacctcggcttaacga
	P._americana    rcgtcgctttca---acgtcgctttcaccaacgtcgctttcacca
	P._myriophylla  acgtcgctttca---acgtcgctttcaccaacgtc?ctttcacca
	P._polygama     acgtcgctctcaccaacgtcgctttcaccaacgtc?ctttcacca
	P._macrophylla  acgtcgctctcaccaacgtcgctttcaccaacgtcgctttcacca
  ;
end;

begin characters;
LINK TAXA= second;
  title second_chars;
	dimensions nchar=45;
  format datatype=rna missing=? 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 characters = bogus; 
	tree one = [&U] ('P. fimbriata',
	'X. robusta',
	(		'P. americana',
		'N. myriophylla'
	)
	'P. polygama',
	'P. macrophylla');
end;
begin trees;
LINK TAXA= firstt characters = bogus; 
	title second_trees;
	tree one = [&U] ('P. fimbriata',
	'P. robusta',
	(		'P. americana',
		'P. myriophylla'
	));
end;
begin assumptions;
	title mixedupassump;
	TAXSET  o(TAXA=firstt) = P._fimbriata P._robusta  ;
	CHARSET o (Characters=second_chars)= 1-5 7 9 11 12-24\2  30-.\5;
	CHARSET p  (Characters=firstchars Standard) = 2- 7 9-11 12-24\2  44-. ;
	TAXSET  p (Standard TAXA=second) = 1 - . \2;
	CHARSET r  (Characters=firstchars) = 2- 8 9-11   44-.  12-24\3;
end;
begin assumptions;
	title explicit;
    LINK TAXA = firstt CHARACTERS = 'second chars';
	TAXSET o = P._fimbriata P._robusta  ;
	CHARSET oe = 1-5 7 9 11 12-24\2  30-.\5;
end;
begin assumptions;
	title explicit2;
    LINK TAXA = second CHARACTERS = firstchars;
	CHARSET pe = 2- 7 9-11 12-24\2  44-. ;
	TAXSET pe = p 2;
	
end;


