#nexus

begin taxa;
  dimensions ntax=6;
  taxlabels
	'P. fimbriata'
	'P. robusta'
	'P. americana'
	'P. myriophylla'
	'P. polygama'
	'P. macrophylla'
  ;
  blockid bogus;
end;

[!
*************
* dna       *
*************
]
begin characters;
  dimensions nchar=45;
  format datatype=dna missing=? gap=-;
  title dna_forty_five;
	CHARLABELS labone labtwo labthree labfour labfive labsix labseven;

  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 trees;
	tree treone = (1,2,3,4,5,6);
	tree tretwo = (1,(2,3),4,5,6)[test];
	tree trethr = (1,2,(3,4),5,6);
end;
BEGIN Sets;
    Charset csone = 1-3;
    CHARPARTITION csparttwo (STANDARD CHARACTERS='dna forty five') = firstthree: csone, next: 4-12\2, anothergr : 5 - . \2 , rest : 14 - 44\2;
    CHARPARTITION cspart (STANDARD CHARACTERS='dna forty five') = firstthree: csone, next: 4-14\2, anothergr : 5 - . \2 , rest : 16 - 44\2;
    TaxPARTITION cspart = firstthree: P._fimbriata-3, next: 4, anothergr : 6 , rest : 5;
    TreePARTITION cspart=next:3,firstthree:1-2;
end; BEGIN ASSUMPTIONS;
	Usertype mine (stepmatrix) = 4 a c g t . 1 1 1 2 . 2 2 3 3 . 3 4 4 4 . ;
    ExSet  e = 3-. \ 4;
    TypeSet * ts = ORD: csone 3-14\2, UNORD: 4-.\2, mine : 15-. \2;
    WtSet  t = 2: csone 3-14\2, 1: 4-.\2, 3 : 15-. \2;
    WtSet  tes = 2: csone 3-14\2, 6.01: 4-.\2, 3 : 15-. \2;
    WtSet * tvecs (vector ) = 1 2  3 1 2 3  1  2 3 
                             1 2  3 1 2 3  11 2 3 
                             1 21 3 1 2 3  1  2 3 
                             1 2  3 1 2 31 1  2 3 
                             1 2  3 1 2 3  1  2 3  ;
    ExSet * edef = 2-. \ 4;
end;
