[BioPython] taxonomic tree

dr goettel biopythonlist at gmail.com
Wed Oct 8 16:23:32 UTC 2008


Hello, I'm new in this list and in BioPython.
I would like to create a NCBI-like taxonomic tree and then fill it with the
organisms that I have in a file. Is there an easy way to do this? I started
using biopython's function at 7.11.4 (finding the lineage of an organism) in
the tutorial, but I need to do this tens of thousands times so it spends too
much time querying NCBI database. Therefore I built a taxonomic database
locally and implemented something similar to 7.11.4 tutorial's function so I
get, for every sequence, the lineage in the same way:

'cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina;
 Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta;
 Liliopsida; Asparagales; Orchidaceae'


Now I need to create a tree, or fill an already created one. And then search
it by some criteria.

Please could anybody help me with this? Any idea?
Thankyou very much



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