[Biopython-dev] [Wg-phyloinformatics] BioGeography update

[Peter]

On Fri, Jul 10, 2009 at 1:07 PM, Brad Chapman<chapmanb at 50mail.com> wrote:
> So, in summary, the major deliverables are:
>
> - Generic tree representation plus a TreeIO structure
> - PhyloXML parser that uses this tree directly
> - Nexus parser that can handle problem files and parse into the
>  generic tree. This will let us drop the lagrange duplication from
>  Nick's code.
>
> Sounds like you have this well worked out,
> Brad

Sounds good. Note PhyloXML (which I gather is annotation rich)
may not have to use the generic trees, it could use a subclass.
If this means the generic trees can be less memory hungry that
might be worth while... something to keep in mind at least. e.g.
Consider a large Newick file with only taxa names and branch
lengths, no branch colours, no bootstraps, no internal node
names, etc.

What specifically is wrong with the Bio.Nexus Newick parser? i.e.
what files won't it parse that the lagrange code will? The only thing
I am aware of is "naked" internal node labels (Bug 2788):
http://bugzilla.open-bio.org/show_bug.cgi?id=2788

Peter