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