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

[Sendu Bala]

Chris Fields wrote:
>
> 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

Indeed. The two can be considered closely intertwined - if you were 
making a phylogeny you might hang it on a taxonomy. At any rate, you 
need to know a bunch of evolutionarily related species names before you 
start work, and Bio::Taxonomy::Node has been as good a place as any to 
get that.


> 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

Which is why the Trees HOWTO talks about taxa, and a number of the 
Taxonomy modules have phylogenetic methods like get_lca. (And why there 
is Bio::Taxonomy::Taxon and Tree.)

I suppose this is another reason to make Bio::Taxonomy::Node (ne 
Bio::Taxon) implement Bio::Tree::NodeI.

(for these reasons I don't think Gabriel's method isn't best appropriate 
as a script - it's something you might do all the time, as a matter of 
course. If Bio::Taxon wasa Bio::Tree::NodeI you would just do my $tree = 
new Bio::Tree::Tree(-root => $bio_taxon); and blamo, instant 
phylogenetic taxonomy)