---
name: "bp_taxonomy2tree"
section: "1p"
platform: "linux"
package: "bioperl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bp_taxonomy2tree"
---

# bp\_taxonomy2tree(1p)

Building a taxonomic tree based on the full lineages of a set of species names

## 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