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Python implementation of codon adaptation index

Project description

Python Codon Adaptation Index
|DOI| |Docs| |Travis| |CodeFactor| |PyPI|

An implementation of `Sharp and Li's 1987
formulation <>`_
of the `codon adaption index


This module is available from PyPI and can be downloaded with the following command::

$ pip install CAI

To install the latest development version::

$ pip install git+

.. _quickstart:


Finding the CAI of a sequence is easy::

>>> from CAI import CAI
>>> CAI("ATG...", reference=["ATGTTT...", "ATGCGC...",...])

Similarly, from the command line::

$ CAI -s sequence.fasta -r reference_sequences.fasta

Determining which sequences to use as the reference set is left to the user,
though the `HEG-DB <>`_ is a great resource of
highly expressed genes.

Contributing and Getting Support

If you encounter any issues using CAI, feel free to `create an issue

To contribute to the project, please `create a pull request
<>`_. For more
information on how to do so, please look at GitHub's `documentation on pull
requests <>`_.


Lee, B. D. (2018). Python Implementation of Codon Adaptation Index. *Journal of
Open Source Software, 3*(30), 905. `

doi = {10.21105/joss.00905},
url = {},
year = {2018},
month = {oct},
publisher = {The Open Journal},
volume = {3},
number = {30},
pages = {905},
author = {Benjamin D. Lee},
title = {Python Implementation of Codon Adaptation Index},
journal = {Journal of Open Source Software}


I'm available for contact at
` <>`_.


Sharp, P. M., & Li, W. H. (1987). The codon adaptation index--a measure of
directional synonymous codon usage bias, and its potential applications.
*Nucleic Acids Research*, 15(3), 1281–1295.

.. |DOI| image::

.. |Docs| image::
:alt: Documentation Status

.. |Travis| image::

.. |CodeFactor| image::

.. |PyPI| image::

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