xenial (1) bp_taxonomy2tree.1p.gz

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