[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

2009/11/2 Richard Holland <holland at eaglegenomics.com>:
> The graphs returned by the Nexus parser are instances that implement the
> org.jgrapht.UndirectedGraph interface. Undirected graphs have no root.


Yes, that is a property of the jgrapht. But it might not be the case
of the original nexus file/tree. So, if the tree is rooted, how can
one know the root (without doing the parsing again ourselves to
discover it)? I note two things:
a) The root is obviously not one taxa, but one intermediate node.
b) Even if the tree is unrooted, it might be interesting to know the
"root", for instance to draw the tree, in the way that is was written
in the file.

Tiago
PS - I also added to bugzilla one but related to the parser, but that
is different problem...