Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
See also What’s new.
All supported versions of Python 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 remove older versions of Biopython and NumPy before it installs the recent versions.
Should you wish to uninstall Biopython:
pip uninstall biopython
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:
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:\Python36\Scripts\pip install biopython
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 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.
python.hsetuptools, gcc will work fine on
UNIX-like platforms. This is not needed on Windows if using the
compiled packages provided. 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:
Recent releases of Biopython require NumPy (and not Numeric). Version 1.76 is the last release to support Python 2.7 and 3.5, all later releases require Python 3.6 or greater:
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.