BP_TAXONOMY2TREE(1) User Contributed Perl Documentation BP_TAXONOMY2TREE(1)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
perl v5.14.1 2011-07-22 BP_TAXONOMY2TREE(1)
