cogent3 is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for manipulation of genomic sequence data and for conducting molecular evolutionary analyses. It is distinguished by many unique built-in capabilities. Of particular note are our non-stationary Markov substitution models. These include non-stationary nucleotide and non-stationary codon models.



All the code presented in this documentation is working, but does not reflect the current best-practice. The documentation will be significantly revised in the next couple of months.

Posting Bugs

If you discover a bug please post a ticket at the issues page!


If you use this software for published work please cite – Knight et al., 2007, Genome Biol, 8, R171.


We acknowledge the provision by Wingware of free licenses for their professional IDE. Their commitment, over more than a decade, to supporting our development of Open Source software for science is greatly appreciated. (The port of PyCogent to Python 3 was made much easier by using Wing’s refactor tools!)