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Christopher Fields
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bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names


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