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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 v5.24.1			  2017-07-08		   BP_TAXONOMY2TREE(1)

NAME | DESCRIPTION | AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala

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