[Biojava-l] Rooted trees in nexus files

[Tiago Antão]

2009/11/2 Richard Holland <holland at eaglegenomics.com>:
> In the meantime, the JGraph library which is used for displaying JGraphT
> graphs in a visual form does include root-finding methods, so maybe you
> could investigate there to see if any of the existing functions might help?

Did that. None can help as the graph is not directed (it would be
trivial with a directed graph ,of course).
In the current form, the nexus parser is of limited use for tree information:
1. For rooted trees it has a bug has it doesn't say what is the root
2. For unrooted trees, sometimes the "root" (what the user perceives
as root) is interesting information.

Tiago