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

[Chris Fields]

Now I get personal email?  Yikes!

Sendu has indicated that Bio::DB::Taxonomy will stay essentially unchanged.
If anything changes, it >may< be the class used to hold the Node
information.  

Would be nice to know how you use Bio::Taxonomy.  You are the first here who
seems to have a use for it.

As for branch lengths, I think you're confusing 'taxonomy' (classification
of organisms based on just about anything) with 'phylogeny' (evolutionary
relatedness).  Note in the Wikipedia article below the use of the term
'phylogenetic taxonomy', which is the classification of organisms based on
evolutionary relationships.

http://en.wikipedia.org/wiki/Taxonomy

http://en.wikipedia.org/wiki/Phylogeny

NCBI has a disclaimer about the Taxonomy database that is related to this:

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=how
cite

There are HOWTOs on tree manipulation, population genetics, and PAML on the
wiki which might be a good start for Bioperl phylogenetic methods:

http://www.bioperl.org/wiki/HOWTO:Trees

http://www.bioperl.org/wiki/HOWTO:PAML

http://www.bioperl.org/wiki/HOWTO:PopGen


Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Gabriel Valiente
> Sent: Friday, July 28, 2006 7:10 AM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes (Chris Fields)
> 
> >>> At the moment it seems to me that the Bio::Taxonomy modules
> >>> (excluding
> >>> Node) aren't really usable.
> 
> I've been using Bio::Taxonomy 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.
> 
> BTW, does anybody know how to include branch lengths in
> Bio::DB::Taxonomy?
> 
> Thanks a lot,
> 
> Gabriel
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