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BP_TAXONOMY2TREE

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 AT lsi DOT upc DOT edu Email bix AT sendu DOT me DOT uk

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