Skip to content
Command line taxonomy browser
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


Command line NCBI/ENA taxonomy browser


taxo is a command line utility to query a local copy of the NCBI taxonomy database. It can look up taxons by their NCBI/ENA taxonomy identifier, name, regex, and so on. It can present various sets of information for the taxon.

Taxo can also operate interactively (taxo-browser), allowing you to navigate the taxonomy tree from the command line.

taxo and taxo-browser use taxo-db as their back-end. taxo-db imports the NCBI taxdump archive and offers a SQL interface to query the taxonomy database.

Taxo is lightweight and requires no special installation.

In case you wonder why I don't just use the Taxonomy browser or Taxonomy Common Tree at NCBI Taxonomy: this may explain. In my corner of the world, we have the intermittentnet.

Home: (previously part of blast-galley).


  • Prerequisites

    Taxo requires the sqlite3 and awk programs. These are often already present on your system, or else easily installable. On Debian/Ubuntu:

    sudo apt-get install sqlite3 awk

    If you want to search using regular expressions, then install the PCRE extension for sqlite3:

    sudo apt-get install sqlite3-pcre awk
  • Clone the repository

    git clone
    cd taxo
    ./taxo --help
  • Import the taxonomy database

    The import may yield warnings and errors; the taxdump file format is a mess. The database is installed in ~/.taxo-db.

    ftp '' | ./taxo-db -v -i -
  • [Optional] Add taxo to your path

    No further installation is needed. For convenience you could add taxo's directory to your PATH, or symlink the taxo script in your ~/bin (assuming it is on your PATH, which it is on many systems).


The taxo, taxo-browser, and taxo-db commands are self-contained. Invoke with --help to see usage instructions. Below are some examples to get you going.

Examples: Command-line Use

Searching on taxonomic name

$ ./taxo Zika
64320   species Zika virus
186278  species Cottus kazika
1756945 species Henneguya zikaweiensis
1879016 species Zika virus vector pZIKV-ICD

Regular expression search

$ taxo -r '.*monas$'
85      genus   Hyphomonas
226     genus   Alteromonas
283     genus   Comamonas

Also search the alternative (non-scientific) names:

$ taxo -a hydrophilia'
644     species Aeromonas hydrophilia   misspelling

Looking up on taxid:

$ taxo 286 666
    286 genus        Pseudomonas
    666 species      Vibrio cholerae

Retrieve citations

$ taxo -c 666
666     species Vibrio cholerae 2759    Skerman VBD et al. (1980)  ...
666     species Vibrio cholerae 3356    Lapage SP et al. (1992) ...
666     species Vibrio cholerae 9485    Nandi S et al. (1997) ...

Retrieve lots of information

$ taxo -x 777
... wide tab separated datasheet ...

Examples: Interactive Use

The interactive taxo-browser has the same functionality, with the added convenience of being able to navigate a pointer up and down the tree, and examine ancestors, siblings, or descendants in each context.

$ ./taxo

Command? help

-                ENTER key displays current node ID, rank and name
- NUMBER         jump to node with taxid NUMBER
- /REGEX         search for nodes whose name matches left-anchored REGEX
- u(p)           move current node pointer to parent node
- p(arent)       show parent but do not move current node pointer there
- a(ncestors)    show lineage of current node all the way up to root
- s(iblings)     show all siblings of the current node
- c(hildren)     show all children of the current node
- D(escendants)  show all descendants of the current node
- q(uit) or ^D   leave

Command? /Acinetobacter baumannii$
    470 species      Acinetobacter baumannii

Command? 1279
   1279 genus        Staphylococcus

Command? s
  45669 genus        Salinicoccus
 370802              environmental samples
 227979 genus        Jeotgalicoccus
1647178 genus        Aliicoccus
 489909 genus        Nosocomiicoccus
  69965 genus        Macrococcus
 111016              unclassified Staphylococcaceae
   1279 genus        Staphylococcus

Command? c
   1280 species      Staphylococcus aureus
   1281 species      Staphylococcus carnosus
   1282 species      Staphylococcus epidermidis
   ...    ...


taxo - Command line taxonomy browser
Copyright (C) 2016 Marco van Zwetselaar

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see

You can’t perform that action at this time.