#nexus

[!Output comment before first block]

begin paup; [this is an unknown block]
	lset nst=2 basefreq=empirical tratio=estimate rates=gamma shape=estimate;
end;

[!Let's see if we can deal with [nested] comments]

[!
What happens if we do this!
]

begin [comment at beginning of token]taxa;
	dimensions[comment at end of token] ntax=11;
	taxlabels  [comment between tokens]
		P._fimbriata
		'P. robusta'
		'P. americana'
		'P. myriophylla'
		'P. articulata'
		'P. parksii'
		'P. gracilis'
		'P. macrophylla'
		'P. polygama'
		'P. basiramia'
		'P. ciliata'
		[!output comment in TAXLABELS command]
	;
end;

begin trees;
	translate
		1  P._fimbriata,
		2  P._robusta,
		3  P._americana,
		4  P._myriophylla,
		5  P._articulata,
		6  P._parksii,
		7  P._polygama,
		8  P._macrophylla,
		9  P._gracilis,
		10  P._basiramia,
		11  P._ciliata
	;
	utree unrooted =      (1,2,((4,3,(5,6)),((7,8),(9,(10,11)))));
	tree  rooted   =      ((1,2),((4,3,(5,6)),(7,(8,(9,(10,11))))));
	utree u_to_r   = [&R] ((1,2),((4,3,(5,6)),(7,(8,(9,(10,11))))));
	tree  r_to_u   = [&U] (1,2,((4,3,(5,6)),((7,8),(9,(10,11)))));
end;
