As per our Downloads Page page, we generally recommend using Python’s package manager pip to install Biopython:

pip install biopython

However, this is not the only option and a separate packaging system may be more appropriate for your system.

Conda

If your Python is installed using conda, for example using miniconda or anaconda, then you should be able to use Biopython from the conda packages:

conda install -c conda-forge biopython

or:

conda update -c conda-forge biopython

We deliberately recommend using Biopython from the conda-forge channel, as this is usually up to date and covers Windows, Mac OS X and Linux. The default Conda channel does have Biopython, but is often out of date.

Note Conda is available on Windows, Mac OS X and Linux, and covers far more than just Python.

Linux Packages

Although we would generally recommend pip, most Linux systems will have a Biopython package available - it may however by a little out of date.

Ubuntu or Debian

You should be able to install Biopython and its dependencies using the Synaptic GUI tool (on the main menu under System / Administration / Synaptic Package Manager), or at the command line using:

sudo apt-get install python-biopython

If you want the documentation and unit tests,

sudo apt-get install python-biopython-doc

And if you want to use BioSQL,

sudo apt-get install python-biopython-sql

However, this will probably not be the latest release (see Ubuntu listing here, and Debian listing here). If you want the latest version of Biopython, you will need to install it from source. However, you should be able to automatically install the build dependencies with the following command:

sudo apt-get build-dep python-biopython

Archlinux

Biopython is in the official Archlinux repository as python-biopython (for Python 3) or python2-biopython (for Python 2) and can be installed using pacman:

pacman -S python2-biopython

Or, for Python 3:

pacman -S python-biopython

Fedora

Biopython is an official Fedora package (since Fedora 5). The package is named python-biopython for Python 2, or python3-biopython for Python 3, and can be installed using yum as root:

yum install python-biopython

or

yum install python3-biopython

or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).

Gentoo Linux

Gentoo’s portage tree contains an ebuild (sci-biology/biopython) which builds from source. To install it, open a terminal as root and run:

emerge -va biopython

Here is a link to Biopython at Gentoo which shows the latest versions in Gentoo’s Portage tree.

Other Unix-like systems

FreeBSD and Ports

The most easy way of installing Biopython in FreeBSD is through the Ports Collection. If you’re new to this procedure please take a look at this document. Supposing that you’re familiar with this method and that you have an up-to-date ports tree, all you need to do is to execute the following commands as root:

cd /usr/ports/biology/py-biopython make install clean

This should automatically fetch and install Biopython (as well as its necessary dependencies).