Python Tools for Computational Molecular Biology

Biopython version 1.70
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Current Release - 1.70 - 10 July 2017

See also What’s new.

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Biopython 1.70

Installation Instructions

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 python and pip are not on the PATH. 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

Other packages

While we generally recommend using pip to install Biopython using the wheel packages we provide on PyPI (as above), there are also Biopython packages for Conda, Linux, etc.

Installation from Source

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:

xcode-select --install

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:

python setup.py build
python setup.py test
python setup.py install

or:

pip install .

If you are still stuck, sign up to the Biopython mailing list and ask for help there.

Required Software

Optional Software

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:

Old Releases

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.