:orphan:



.. _sphx_glr_draw:

#############
Image Gallery
#############

We use `Plotly <https://plotly.com/python/>`_ as our backend for visualisation. It provides excellent graph interactivity in Jupyter notebooks.


.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_draw_aln:

**********************
Alignments & Sequences
**********************




.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A method on the alignment provides an interface to the simpler (and yet robust and fast) method...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-coevolution_thumb.png
     :alt: Evaluating coevolution

     :ref:`sphx_glr_draw_aln_plot_aln-coevolution.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-coevolution

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A technique (`Gibbs and McIntyre &lt;https://www.ncbi.nlm.nih.gov/pubmed/5456129&gt;`_) for comparing...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-dotplot-1_thumb.png
     :alt: Dotplot

     :ref:`sphx_glr_draw_aln_plot_aln-dotplot-1.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-dotplot-1

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="If sequences in a dotplot have been annotated, the dotplot() method returns an AnnotatedDrawabl...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-dotplot-2_thumb.png
     :alt: Dotplot with annotated sequences

     :ref:`sphx_glr_draw_aln_plot_aln-dotplot-2.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-dotplot-2

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="We have several different ways of counting sequence gaps, and of visualising the results. By de...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-gaps-per-seq_thumb.png
     :alt: Counting gaps per sequence

     :ref:`sphx_glr_draw_aln_plot_aln-gaps-per-seq.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-gaps-per-seq

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Information here is in the formal sense -- maximum entropy minus the entropy at a position. Thi...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-info-plot_thumb.png
     :alt: Information analysis of an alignment

     :ref:`sphx_glr_draw_aln_plot_aln-info-plot.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-info-plot

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Sequence logo&#x27;s display sequence information. They&#x27;re extensively applied to transcription fact...">

.. only:: html

 .. figure:: /draw/aln/images/thumb/sphx_glr_plot_aln-seqlogo_thumb.png
     :alt: Draw sequence logos

     :ref:`sphx_glr_draw_aln_plot_aln-seqlogo.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/aln/plot_aln-seqlogo
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. _sphx_glr_draw_tree:

******************
Phylogenetic Trees
******************




.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This is a left-right style. You&#x27;ll note that there&#x27;s overlap of edges at the bottom -- a known ...">

.. only:: html

 .. figure:: /draw/tree/images/thumb/sphx_glr_plot_tree-angular_thumb.png
     :alt: Display a Phylogenetic Tree with a Angular Dendrogram Style

     :ref:`sphx_glr_draw_tree_plot_tree-angular.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/tree/plot_tree-angular

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Display a Phylogenetic Tree with a Circular Dendrogram Style">

.. only:: html

 .. figure:: /draw/tree/images/thumb/sphx_glr_plot_tree-circular_thumb.png
     :alt: Display a Phylogenetic Tree with a Circular Dendrogram Style

     :ref:`sphx_glr_draw_tree_plot_tree-circular.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/tree/plot_tree-circular

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Display a Phylogenetic Tree with a Radial Dendrogram Style">

.. only:: html

 .. figure:: /draw/tree/images/thumb/sphx_glr_plot_tree-radial_thumb.png
     :alt: Display a Phylogenetic Tree with a Radial Dendrogram Style

     :ref:`sphx_glr_draw_tree_plot_tree-radial.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/tree/plot_tree-radial

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="We use a tree saved in json format from a likelihood function analysis of a non-stationary mode...">

.. only:: html

 .. figure:: /draw/tree/images/thumb/sphx_glr_plot_tree-square_thumb.png
     :alt: Display a Phylogenetic Tree with a Square Dendrogram Style

     :ref:`sphx_glr_draw_tree_plot_tree-square.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/tree/plot_tree-square

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="We use a tree saved in json format from a 100 replicate bootstrap resamplings. The show_support...">

.. only:: html

 .. figure:: /draw/tree/images/thumb/sphx_glr_plot_tree-support_thumb.png
     :alt: Display a Phylogenetic Tree Showing Bootstrap Support

     :ref:`sphx_glr_draw_tree_plot_tree-support.py`

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /draw/tree/plot_tree-support
.. raw:: html

    <div class="sphx-glr-clear"></div>



.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_
