.. _contents: .. warning:: We will soon stop using Read The Docs for our latest documentation. Please check the cogent3_ github page for the up-to-date link! #################### ``cogent3`` Overview #################### 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 `_, .. raw:: html and `non-stationary codon `_ models. Plus, the ability to manipulate biological sequences by their annotations. .. raw:: html .. toctree:: :hidden: :maxdepth: 2 warning install app/index draw/index library licenses general .. _cogent3: https://github.com/cogent3/cogent3