BP_TAXONOMY2TREE(1)

✨ NAME ✨

okay so bp_taxonomy2tree is literally the tool that builds a taxonomic tree based on the full lineages of a set of species names, periodt. This is the bp_taxonomy2tree(1) page, straight from User Contributed Perl Documentation 🫶.

💖 DESCRIPTION 💖

Bestie, here’s the vibe: this script looks up the species names you give it in the NCBI Taxonomy database, retrieves their full lineage, and puts them in a Newick taxonomic tree displayed on screen. iconic. ✨

Like, for real:

bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human
bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

You can also provide:

• -d — specify the directory to store index files in 🗂️
• -o — specify the location of your NCBI nodes file 📍
• -a — for the NCBI names file 📛
• -e — 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. yes, that’s required, no cap 💅.

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 — like, go get a snack, bestie 😭. However once created, these indexes will allow fast access for species to taxon id OR taxon id to species name lookups. slay. 🔥

👑 AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala 👑

• Email valiente@lsi.upc.edu
• Email bix@sendu.me.uk

xoxo, this page is serving User Contributed Perl Documentation energy from perl v5.42.3, dated 2021-02-03, and it’s called BP_TAXONOMY2TREE(1) 💖🎀