cogent3 is a software library for genomic biology. It is a comprehensive 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.

Plus, the ability to manipulate biological sequences by their annotations.

cogent3 apps

cogent3 comes with pre-defined “apps” that simplify otherwise complex tasks. They provide capabilities that can be used by themselves, or added together to define a pipeline. They also simplify parallel execution of pipelines.


The cookbook presents short code recipes targeted at specific problems.


The tutorials present code for solving more extensive problems.


The API for major cogent3 objects