scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
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ElDeveloper and thermokarst TST: Ship a pytest runner with every installation (#1633)
Moves the test runner from being a setup command to being a module-level
function. In this patch I also removed the additional configuration
files and make all necessary configurations through the file
and the runner's arguments.

All this is necessary so we can properly test skbio upon building it
using conda.
Latest commit de756f0 Oct 1, 2018
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assets ENH: add inverted vector logo Jul 2, 2015
benchmarks BUG: fix performance regression by reinstating empty metadata optimiz… Jun 7, 2016
ci TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018
doc DOC: update documentation building to use napoleon (#1629) Sep 21, 2018
ipynbs/presentations From upstream May 2, 2015
licenses skbio.metadata.IntervalMetadata, skbio.metadata.Interval objects (#1414) Sep 6, 2016
skbio TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018
.coveragerc ENH: improved Sequence repr Jun 26, 2015
.gitignore MAINT: Remove invisible file and add to gitignore Jul 14, 2015
.travis.yml TST: test runner is now pytest ( 👃) (#1624) Sep 21, 2018 Add composition functions alr and sbp (#1601) Sep 9, 2018 TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018
COPYING.txt MAINT: added names in place of placeholder Jun 17, 2014 TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018
Makefile TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018 DOC/BUG: fix links in PR template (#1468) Nov 29, 2016
README.rst MAINT: update version to 0.5.2-dev (#1565) Apr 25, 2018 DOC: update release document (#1463) Nov 28, 2016 DOC: add code review doc (#1464) Nov 29, 2016
asv.conf.json DOC: update docs to reflect Python 3-only support Mar 25, 2016 CI/ENH: add directive to to ignore copyright header vali… Sep 2, 2016 TST: Ship a pytest runner with every installation (#1633) Oct 1, 2018


scikit-bio logo

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scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics.

To view scikit-bio's documentation, visit

Note: scikit-bio is no longer compatible with Python 2. scikit-bio is compatible with Python 3.4 and later.

scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear to users when an API can be relied upon (stable) and when it may be subject to change (experimental). See the API stability docs for more details, including what we mean by stable and experimental in this context.


The recommended way to install scikit-bio is via the conda package manager available in Anaconda or miniconda.

To install the latest release of scikit-bio:

conda install -c conda-forge scikit-bio

Alternatively, you can install scikit-bio using pip:

pip install numpy
pip install scikit-bio

You can verify your installation by running the scikit-bio unit tests:

python -m skbio.test

For users of Debian, skbio is in the Debian software distribution and may be installed using:

sudo apt-get install python3-skbio python-skbio-doc

Getting help

To get help with scikit-bio, you should use the skbio tag on StackOverflow (SO). Before posting a question, check out SO's guide on how to ask a question. The scikit-bio developers regularly monitor the skbio SO tag.

Projects using scikit-bio

Some of the projects that we know of that are using scikit-bio are:

If you're using scikit-bio in your own projects, feel free to issue a pull request to add them to this list.

scikit-bio development

If you're interested in getting involved in scikit-bio development, see

See the list of scikit-bio's contributors.


scikit-bio is available under the new BSD license. See COPYING.txt for scikit-bio's license, and the licenses directory for the licenses of third-party software that is (either partially or entirely) distributed with scikit-bio.

The pre-history of scikit-bio

scikit-bio began from code derived from PyCogent and QIIME, and the contributors and/or copyright holders have agreed to make the code they wrote for PyCogent and/or QIIME available under the BSD license. The contributors to PyCogent and/or QIIME modules that have been ported to scikit-bio are: Rob Knight (@rob-knight), Gavin Huttley (@gavin-huttley), Daniel McDonald (@wasade), Micah Hamady, Antonio Gonzalez (@antgonza), Sandra Smit, Greg Caporaso (@gregcaporaso), Jai Ram Rideout (@jairideout), Cathy Lozupone (@clozupone), Mike Robeson (@mikerobeson), Marcin Cieslik, Peter Maxwell, Jeremy Widmann, Zongzhi Liu, Michael Dwan, Logan Knecht (@loganknecht), Andrew Cochran, Jose Carlos Clemente (@cleme), Damien Coy, Levi McCracken, Andrew Butterfield, Will Van Treuren (@wdwvt1), Justin Kuczynski (@justin212k), Jose Antonio Navas Molina (@josenavas), Matthew Wakefield (@genomematt) and Jens Reeder (@jensreeder).


scikit-bio's logo was created by Alina Prassas.