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#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;
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