[Bioperl-l] Bio::*Taxonomy* changes (Chris Fields)

[Sendu Bala]

Gabriel Valiente wrote:
>>>> At the moment it seems to me that the Bio::Taxonomy modules  
>>>> (excluding
>>>> Node) aren't really usable.
> 
> I've been using Bio::Taxonomy

Can I ask how you've been using it?


> and Bio::DB::Taxonomy a lot, they are  
> very useful modules. Whatever Bio::Taxon or Bio::Taxonomy::Taxon  
> turns out to be, please do keep the Bio::DB::Taxonomy functionality.

Bio::DB::Taxonomy is staying virtually unaltered.


> BTW, does anybody know how to include branch lengths in  
> Bio::DB::Taxonomy?

At the moment, you don't 'include' anything at all in the DB modules 
yourself, since they are read-only. They give you Nodes which you can 
alter afterwards.

I plan to add something like a 'distance to parent' in Node (Bio::Taxon) 
so you can work out branch lengths; you can't do that yet.