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.IX Title "BP_TAXONOMY2TREE 1p"
.TH BP_TAXONOMY2TREE 1p "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
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.SH "NAME"
bp_taxonomy2tree \- Building a taxonomic tree based on the full lineages of a set of species names
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This scripts looks up the provided species names in the \s-1NCBI\s0 Taxonomy database,
retrieves their full lineage and puts them in a Newick taxonomic tree displayed
on screen.
.PP
.Vb 2
\&  bp_taxonomy2tree.pl \-s Orangutan \-s Gorilla \-s Chimpanzee \-s Human
\&  bp_taxonomy2tree.pl \-s Orangutan \-s Gorilla \-s Chimpanzee \-s "Homo Sapiens"
.Ve
.PP
Can also provide \-d to specify the directory to store index files in, \-o to
specify the location of your \s-1NCBI\s0 nodes file, and \-a for the \s-1NCBI\s0 names file.
Or the option \-e to use the web-based Entrez taxonomy database if you do not
have the \s-1NCBI\s0 flatfiles installed.
.PP
This script requires that the bioperl-run pkg be also installed.
.PP
Providing the nodes.dmp and names.dmp files from the \s-1NCBI\s0 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 \s-1OR\s0 taxon id to species name
lookups.
.SH "AUTHOR \- Gabriel Valiente, reimplemented by Sendu Bala"
.IX Header "AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala"
Email valiente@lsi.upc.edu
Email bix@sendu.me.uk