See also What’s new.
Note we don’t (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has kindly made Windows 64bit installers for NumPy and Biopython (and other tools) available for testing.
For Windows 32-bit we provide click-and-run installers (specific to your version of Python), but you will first need to install some prerequisite software (listed below, in particular, NumPy).
For Windows 64-bit we recommend the click-and-run Windows 64bit installers (specific to your version of Python) kindly provided by Christoph Gohlke.
Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.
Recent version of Python (starting with Python 2.7.9 and Python 3.4) include
the Python package management tool
pip, which allows an easy installation
on all plattforms. Try:
pip install biopython
Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:
python setup.py build python setup.py test sudo python setup.py install
Substitute python with your specific version, for example python3, jython or pypy.
For Mac OS X, we recommend installing from source as above. You will need to have installed Apple’s XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI’s options menu, or on Mavericks by using the command:
If you have trouble, see the full installation instructions:
If you are still stuck, sign up to the Biopython mailing list and ask for help there.
distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, you should install Apple’s XCode including the command line tools.
Some parts of Biopython use the following additional python libraries:
In addition Biopython includes wrapper code for calling a number of third party command line tools including:
For those of you using Linux, the easiest way to install Biopython is through your distribution’s package management system. However, unless you are running a recent release of your Linux Distribution, you may find that the Biopython packages available to be a little out of date. You might want to see if there is a backport available, otherwise you will have to install Biopython from source.
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
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
Biopython is an official Fedora package (since Fedora 5). The package is named python-biopython, and can be installed using yum as root:
yum install python-biopython
or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).
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
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
Due to the great architecture of the ports system, this simple commands will automatically fetch and install Biopython (as well as its necessary dependencies).
Recent releases of Biopython require NumPy (and not Numeric):
Please note that Biopython 1.48 and older require the Numeric library, not its replacement NumPy. Windows installers for Python 2.4 and older are available from the Numerical Python website. A Windows installer for Numeric 24.2 for Python 2.5 is available here:
Please note that Biopython 1.48 and older used mxTextTools 2.0 in some of the parsers. There were a few niggles with mxTextTools 3.0, so ideally install the older mxTextTools 2.0.