BP_TAXONOMY2TREE(1) User Contributed Perl Documentation BP_TAXONOMY2TREE(1)NAME
bp_taxonomy2tree - Building a taxonomic tree based on the full lineages
of a set of species names
DESCRIPTION
This scripts looks up the provided species names in the NCBI Taxonomy
database, retrieves their full lineage and puts them in a Newick
taxonomic tree displayed on screen.
bp_taxonomy2tree.pl-s Orangutan -s Gorilla -s Chimpanzee -s Human
bp_taxonomy2tree.pl-s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"
Can also provide -d to specify the directory to store index files in,
-o to specify the location of your NCBI nodes file, and -a for the NCBI
names file. Or the option -e to use the web-based Entrez taxonomy
database if you do not have the NCBI 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 v5.20.2 2015-09-15 BP_TAXONOMY2TREE(1)
