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#############
Documentation
#############
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 <https://www.ncbi.nlm.nih.gov/pubmed/25503772>`_, and `non-stationary codon <https://www.ncbi.nlm.nih.gov/pubmed/28175284>`_ models.
.. dropdown:: Click to see an animation showing testing a hypothesis involving a non-stationary nucleotide process.
.. raw:: html
<object type="image/gif" data="../_static/gif/demo-fit-ns.gif" style="height: 400px; width: auto;"></object>
Plus, the ability to manipulate biological sequences by their annotations.
.. dropdown:: Click to see an animation showing defining and using sequence annotations.
.. raw:: html
<object type="image/gif" data="../_static/gif/demo-annotate.gif" style="height: 400px; width: auto;"></object>
.. panels::
:header: bg-primary
:footer: text-right
---
``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.
+++++++++++
.. link-button:: app/index
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Cookbook
^^^^^^^^
The cookbook presents short code recipes targeted at specific problems.
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.. link-button:: cookbook/index
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Tutorials
^^^^^^^^^
The tutorials present code for solving more extensive problems.
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.. link-button:: examples/index
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---
API
^^^
The API for major ``cogent3`` objects
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.. link-button:: api/index
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.. toctree::
:hidden:
:maxdepth: 3
app/index
cookbook/index
examples/index
api/index
.. _cogent3: https://cogent3.org
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