

.. _sphx_glr_auto_examples_advanced:

.. advanced_example:

Advanced usage of cocoatree
---------------------------



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="It is possible to perform Cocoatree&#x27;s SCA pipeline by defining it&#x27;s own metric. In this example, we show how to use a callable to compute the coevolution metric.">

.. only:: html

  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_sca_with_own_metric_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_sca_with_own_metric.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Running Cocoatree with your own metric</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we are comparing the results of the co-evolution analysis on serine proteases using SCA and the mutual information.">

.. only:: html

  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_sca_vs_mi_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_sca_vs_mi.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mutual information versus SCA</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows the full process to perform a complete SCA analysis and detect protein sectors from data importation, MSA filtering.">

.. only:: html

  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_full_SCA_analysis_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_full_SCA_analysis.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Perform full SCA analysis on the S1A serine protease dataset</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/advanced/plot_sca_with_own_metric
   /auto_examples/advanced/plot_sca_vs_mi
   /auto_examples/advanced/plot_full_SCA_analysis

