[BioRuby] BioRuby: newick parser

[Pjotr Prins]

Hi Naohisa and others,

I am looking at the Newick/Nexux/PhyloXML parsers at the moment. The
BioRuby ones look rather complete, if not a tad overcomplicated. 

Are you happy with the state of affairs, or do you thing it could be
improved/simplified?  Also, for walking the tree, is the interface now
the one you would choose to implement?

I am asking, because I am looking for the most intuitive way of
parsing and traversing tree information. I see Christian has done a
lot of work in this area (mostly in Java), even to the point of
taking standards forward. Maybe I should ask him? It appears to me we
have solid parsers and data structures. Walking the trees, however,
is less straightforward, and documentation somewhat lacking.

Anyone happy to correct me?

Pj.