.. _sphx_glr_auto_examples_reconstruction:

Reconstruction
^^^^^^^^^^^^^^

Below is a gallery of examples for reconstructing tumor phylogeny using available tools
in :mod:`scphylo.tl`.



.. raw:: html

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

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using PhISCS-BnB on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_bnb_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_bnb`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by PhISCS-BnB</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using Trisicell-Boost on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_booster_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_booster`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by Trisicell-Boost</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using gpps on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_gpps_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_gpps`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by gpps</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using OncoNEM on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_onconem_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_onconem`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by OncoNEM</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using PhISCS on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_phiscs_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_phiscs`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by PhISCS</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using ScisTree on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scistree_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_scistree`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by ScisTree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SCITE on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scite_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_scite`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SCITE</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SiCloneFit on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_siclonefit_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_siclonefit`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SiCloneFit</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SPhyR on a binary single-cell genotype matrix.">

.. only:: html

  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_sphyr_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_sphyr`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SPhyR</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/reconstruction/compute_bnb
   /auto_examples/reconstruction/compute_booster
   /auto_examples/reconstruction/compute_gpps
   /auto_examples/reconstruction/compute_onconem
   /auto_examples/reconstruction/compute_phiscs
   /auto_examples/reconstruction/compute_scistree
   /auto_examples/reconstruction/compute_scite
   /auto_examples/reconstruction/compute_siclonefit
   /auto_examples/reconstruction/compute_sphyr