Free software for biologists

I list here the programs and libraries that I use as a life science researcher. They all run at least on GNU/Linux (and probably most other free systems as well, some also run on MacOS X and/or Windows), and they are all free (“free” as in “free speech”).

I expect most of them should be available as packages on popular GNU/Linux distributions such as Debian and its derivatives. For Slackware users, I provide SlackBuilds for each of these programs.

Name Description License
EMBOSS A collection of small tools addressing a wide range of common molecular biology tasks. A kind of molecular biologist’s Swiss Army knife. Combining several of these tools with a bit of shell script allows to perform efficiently the most complex or tedious manipulations. GPL v2
Acedb (A C. elegans Database) A genome database system. Despite its name, it is not tied to C. elegans (but was originally developped for this organism). Among the tools provided, I am a regular user of dotter, a program to compute and display interactive dot plots. GPL v2 1
MUSCLE A program for creating multiple alignments of protein sequences. Public domain 2
NCBI Toolkit The NCBI Toolkit is the software basis of the various services offered by the National Center for Biotechnology Information. It provides libraries and tools to manipulate biological sequences, most notably all the BLAST-related tools. Public domain 3
Primer3 Primer3 picks primer for PCR reactions, considering various criteria such as oligo melting temperature, size, GC content, size of PCR product, etc. 3-clause BSD
R R is a language and environment for statistical computing and graphics. The language in itself is not oriented towards biology, but many modules specifically dedicated to biology are available. GPL v2
BioPython A set of Python modules for biology. 3-clause BSD-like
OMERO OMERO is a client-server system dedicated to biological image data management and analysis. The server can import and store images and associated metadata coming from most of the available acquisition systems (see Supported Formats for a list of successfully recognized file formats). GPL v2
ImageJ An image processing program; plug-ins for analysis of microscopy data are available. Public domain
Jmol An molecule viewer and editor written in Java; it can be included in a web page as an applet, which makes it particularly suitable for preparing teaching materials. LGPL v2.1
PyMOL Another molecular visualization program, this time written in Python. 3-clause BSD-like
Ugene Ugene offers a single, easy-to-use interface for manipulating biological sequence data. GPL v2
  1. As stated on website and in source files, although the user manual mentions a BSD-like license.
  2. According to the program’s help message.
  3. As a “United States Government Work”.