[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

2009/11/3 Thasso Griebel <thasso.griebel at uni-jena.de>:
> There is a way to uniquely  get a root from a newick string. Usually a
> rooted newick is surrounded with brackets, which indicates the root as the
> highest node in the tree. For example:
>
> (A, (B,C))
>

Agree, it is quite easy to get the root of the tree from the newick
representation. But it should be done on parsing and returned in some
way by the parsing system. If the user has to do it again, it means
that the user has to parse it again just to know the root node.

> I would also suggest to generally parse trees as rooted trees (maybe jsut
> for th initial internal model). Creating an unrooted tree from a rooted  one
> is easy, remove the root and forget about directions. The other way might be
> hard and ambiguous.

100% agree.
The newick _representation_ always has a root by virtue of the way it
is done. If that root has meaning or not depends. Doing as you suggest
seems the most reasonable idea.
I would add that even if it is an unrooted tree, the topology might be
of interest. In my case I am doing a comparative visualizer and it
might be nice for the user to be able to visualize the topology as
specified. It has no biological meaning, but in practice, for many
users, it helps.
I note that PhyloXML (even by virtue of being a XML format) always
represents the phylogenies as trees (not weigthed DAGs). There an
attribute rooted which can be true or false.

But, anyway. Even assuming a very conservative view on this, the
current parser, for rooted trees, does not allow to determine where is
the root. I think that there would be a consensus that that is a bug?

Tiago