Modelling sequence evolution
============================

``cogent3`` possesses unique capabilities for molecular evolutionary analyses. Of particular significance are our non-stationary model classes and the associated measurement of genetic distance from these. That said, we also implement most of the conventional substitution models. See ``cogent3.available_models()`` for a display of the built-in models.

You can use these models either through the general ``model`` app, or some task specific apps. Both are described in the following "how-tos".

.. toctree::
    :maxdepth: 1

    evo-model
    evo-model-with-tree
    evo-model-timehet
    evo-extract-model-stats
    evo-ancestral-states
    evo-dt-nuc-model
    evo-tr-nuc-model
    evo-nstat-codon-model
    evo-tr-codon-model
