See also What’s new.
Recent versions of Python (starting with Python 2.7.9 and Python 3.4) include
the Python package management tool
pip, which allows an easy installation
from the command line on all platforms. Try:
pip install biopython
For updating an older version of Biopython try:
pip install biopython --upgrade
This will delete older versions of Biopython and NumPy before it installs the recent versions.
If pip is not already installed you may need to update your Python, but first try:
python -m ensurepip
If you need to install under a specific version of Python, try something like this:
python2.7 -m pip install biopython python3.6 -m pip install biopython pypy -m pip install biopython
On Windows, by default
pip are not on the
You can re-install Python and tick this option, or give the full path instead.
Try something like this, depending on where your copy of Python is installed:
C:\Python27\Scripts\pip install biopython
Installation from source requires an appropriate C compiler, for example GCC on Linux, and MSVC on Windows. For Mac OS X, or as it is now branded, macOS, if you want to compile Biopython from source you will need to have installed Apple’s command line tools, which can de done with the terminal command:
This will offer to install Apple’s XCode development suite - you can, but it is not needed and takes a lot of disk space.
You can then download and unzip a Biopython source code release, or get our code from GitHub. Then run:
pip install .
If you are still stuck, sign up to the Biopython mailing list and ask for help there.
setuptools, 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 the compiler tools as described above.
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:
We would now recommend
pip, however for those of you using Linux,
you can alternatively install Biopython through your Linux
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find that the Biopython packages available to be a little out of date.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 using
pip or from compiled 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
yum install python-biopython
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’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.