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Freely available tools for computational molecular biology.

Project description

Biopython README file

The Biopython Project is an international association of developers of freely
available Python tools for computational molecular biology.

Our user-centric documentation is hosted on including
the main Biopython Tutorial and Cookbook:
* HTML -
* PDF -

This README file is intended primarily for people interested in working
with the Biopython source code, either one of the releases from the website, or from our repository on GitHub

This Biopython package is open source software made available under generous
terms. Please see the LICENSE file for further details.

If you use Biopython in work contributing to a scientific publication, we ask
that you cite our application note (below) or one of the module specific
publications (listed on our website):

Cock, P.J.A. et al. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3 pmid:19304878

For the impatient

To build and install Biopython, download and unzip the source code, go to this
directory at the command line, and type:

python build
python test
sudo python install

Windows users are instead recommended to use the installation packages provided
on our website.

Python Requirements

We currently recommend using Python 2.7 from which
is the final version of Python 2. Early adopters are encouraged to try
Biopython under Python 3.3 as well.

Biopython is currently supported and tested on the following Python verions:

- Python 2.5, 2.6, 2.7 -- see

This is the currently the primary development platform for Biopython.

- Python 3.3 -- see

Under Python 3 our script calls the 2to3 library automatically
to convert our Python 2 code into Python 3 code. Most of the Biopython
modules are available under Python 3 (but not yet all).

- PyPy 1.9, 2.0 -- see

Aside from modules with C code or dependent of NumPy, everything should
work. Evaluating PyPy's NumPy reimplementation NumPyPy is still in progress.

- Jython 2.5, 2.7 -- see

Aside from modules with C code, or dependent on SQLite3 or NumPy,
everything should work.

Please note that after Biopython 1.62 we will drop support for Python 2.5
and Jython 2.5.


Depending on which parts of Biopython you plan to use, there are a
number of other optional Python dependencies - which can in general
be installed after Biopython.

- NumPy, see (optional, but strongly recommended)
This package is only used in the computationally-oriented modules.
It is required for Bio.Cluster, Bio.PDB and a few other modules. If you
think you might need these modules, then please install NumPy first BEFORE
installing Biopython. The older Numeric library is no longer supported in

- ReportLab, see (optional)
This package is only used in Bio.Graphics, so if you do not need this
functionality, you will not need to install this package. You can install
it later if needed.

- matplotlib, see (optional)
The Bio.Phylo uses this package to plot phylogenetic trees. As with
ReportLab, you can install this at any time to enable the plotting

- networkx, see (optional) and
pygraphviz or pydot, see and (optional)
These packages are used for certain niche functions in Bio.Phylo.
Again, they are only needed to enable these functions and can be installed
later if needed.

- psycopg2, see (optional) or
PyGreSQL (pgdb), see (optional)
These packages are used by BioSQL to access a PostgreSQL database.

- MySQLdb, see (optional)
This package is used by BioSQL to access a MySQL database.

Note that some of these libraries are not available for Jython or PyPy.

In addition there are a number of useful third party tools you may wish to
install such as standalone NCBI BLAST, EMBOSS or ClustalW.


First, **make sure that Python is installed correctly**. Second, we
recommend you install NumPy (see above). Then install Biopython.

Windows users should use the appropriate provided installation package
from our website (each is specific to a different Python version).

Installation from source should be as simple as going to the Biopython
source code directory, and typing:

python build
python test
sudo python install

Substitute `python` with your specific version, for example `python3`,
`jython` or `pypy`.

If you need to do additional configuration, e.g. changing the base
directory, please type `python`, or see the documentation here:
* HTML -
* PDF -


Biopython includes a suite of regression tests to check if everything is
running correctly. To run the tests, go to the biopython source code
directory and type:

python test

Do not panic if you see messages warning of skipped tests:

test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.

This most likely means that a package is not installed. You can
ignore this if it occurs in the tests for a module that you were not
planning on using. If you did want to use that module, please install
the required dependency and re-run the tests.

There is more testing information in the Biopython Tutorial & Cookbook.

Experimental code

Biopython 1.61 introduced a new warning, `Bio.BiopythonExperimentalWarning`,
which is used to mark any experimental code included in the otherwise
stable Biopython releases. Such 'beta' level code is ready for wider
testing, but still likely to change, and should only be tried by early
adopters in order to give feedback via the biopython-dev mailing list.

We'd expect such experimental code to reach stable status within one or two
releases, at which point our normal policies about trying to preserve
backwards compatibility would apply.


While we try to ship a robust package, bugs inevitably pop up. If you are
having problems that might be caused by a bug in Biopython, it is possible
that it has already been identified. Update to the latest release if you are
not using it already, and retry. If the problem persists, please search our
bug database at and our
mailing lists to see if it has already been reported (and hopefully fixed),
and if not please do report the bug. We can't fix problems we don't know
about ;)

If you suspect the problem lies within a parser, it is likely that the data
format has changed and broken the parsing code. (The text BLAST and GenBank
formats seem to be particularly fragile.) Thus, the parsing code in
Biopython is sometimes updated faster than we can build Biopython releases.
You can get the most recent parser by pulling the relevant files (e.g. the
ones in `Bio.SeqIO` or `Bio.Blast`) from our git repository. However, be
careful when doing this, because the code in github is not as well-tested
as released code, and may contain new dependencies.

Finally, you can send a bug report to the bug database or the mailing list at In the bug report, please let us know:

1. Which operating system and hardware (32 bit or 64 bit) you are using
2. Python version
3. Biopython version (or git version/date)
4. Traceback that occurs (the full error message)

And also ideally:

5. Example code that breaks
6. A data file that causes the problem

Contributing, Bug Reports

Biopython is run by volunteers from all over the world, with many types of
backgrounds. We are always looking for people interested in helping with code
development, web-site management, documentation writing, technical
administration, and whatever else comes up.

If you wish to contribute, please visit the web site
and join our mailing list:

Distribution Structure

- README -- This file.
- NEWS -- Release notes and news
- LICENSE -- What you can do with the code.
- CONTRIB -- An (incomplete) list of people who helped Biopython in
one way or another.
- DEPRECATED -- Contains information about modules in Biopython that are
removed or no longer recommended for use, and how to update
code that uses those modules.
- -- Tells distutils what files to distribute
- -- Installation file.
- Bio/ -- The main code base code.
- BioSQL/ -- Code for using Biopython with BioSQL databases.
- Doc/ -- Documentation.
- Scripts/ -- Miscellaneous, possibly useful, standalone scripts
- Tests/ -- Regression testing code

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