[Bioperl-l] Script taxonomy2tree version 1.4 crashed on 110 species

Chris Fields cjfields at uiuc.edu
Mon Dec 18 21:30:04 EST 2006


>> I think you misunderstood me.  The tree is fine; the data used to  
>> make
>> the tree (NCBI taxonomy) is the issue.
>
> In what way is it the issue? The database is also fine as far as I can
> see, in so far as it is not causing any problems in this instance.

I should maybe have clarified a bit more: what I said has nothing to  
do with the structure of the database itself.  I was just pointing  
out that NCBI Taxonomy isn't the best source of data for building a  
phylogenetic tree, something NCBI also points out (the link in my  
last post).  Not a big deal, really.

> Gabriel asked for a tree featuring a species and its subspecies. The
> NCBI taxonomy database provided Bioperl the correct data to build  
> such a
> tree. Then Gabriel asked to remove the degree one nodes of his  
> tree. His
> problem was that doing that happened to (correctly) remove the species
> node. If he wants to see both his species and his subspecies he must
> either not remove degree one nodes, or alter the method of doing so to
> keep desired nodes. There is no possible way for NCBI to improve  
> matters
> here.

Actually, there isn't any way they could w/o digging through the  
literature in many cases.  The problem is incomplete taxonomic  
information for nodes derived from older sequence data, where a genus  
and species was designated but nothing else (strain, etc) is known.

Again, I merely was pointing out what I had mentioned above.  I  
wasn't criticizing you, Gabriel, or the methodology here.  Honest!

chris


More information about the Bioperl-l mailing list