Christopher Fields > BioPerl-1.6.901 > taxonomy2tree

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NAME ^

taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names

DESCRIPTION ^

taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s Human taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

Can also provide -d to specific the directory to store index files in, -o to specific the location of your nodes file, and -a for the names file. Or the option -e to use the web-based entrez taxonomy database if you don't have the flatfiles installed.

This script requires that the bioperl-run pkg be also installed.

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running. This will create the local indexes and may take quite a long time. However once created, these indexes will allow fast access for species to taxon id OR taxon id to species name lookups.

AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala ^

Email valiente@lsi.upc.edu Email bix@sendu.me.uk

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