:orphan:
Examples
========
This section contains various code snippets that demonstrate :mod:`scphylo`'s
usage.
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Reconstruction
^^^^^^^^^^^^^^
Below is a gallery of examples for reconstructing tumor phylogeny using available tools
in :mod:`scphylo.tl`.
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_bnb_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_bnb.py`
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Reconstruct tree by PhISCS-BnB
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_booster_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_booster.py`
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Reconstruct tree by Trisicell-Boost
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_gpps_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_gpps.py`
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Reconstruct tree by gpps
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_onconem_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_onconem.py`
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Reconstruct tree by OncoNEM
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_phiscs_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_phiscs.py`
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Reconstruct tree by PhISCS
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scistree_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_scistree.py`
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Reconstruct tree by ScisTree
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scite_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_scite.py`
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Reconstruct tree by SCITE
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_siclonefit_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_siclonefit.py`
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Reconstruct tree by SiCloneFit
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.. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_sphyr_thumb.png
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:ref:`sphx_glr_auto_examples_reconstruction_compute_sphyr.py`
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Reconstruct tree by SPhyR
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Comparison
^^^^^^^^^^
Below is a gallery of examples for comparing two phylogenetic trees using available
tools in :mod:`scphylo.tl`.
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_ad_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_ad.py`
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Comparing two trees by Ancestor-Descendent
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_caset_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_caset.py`
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Comparing two trees by CASet
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_disc_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_disc.py`
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Comparing two trees by DISC
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_dl_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_dl.py`
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Comparing two trees by Different-Lineage
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_gs_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_gs.py`
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Comparing two trees by Genotype-Similarity
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_mltd_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_mltd.py`
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Comparing two trees by MLTD
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_mp3_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_mp3.py`
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Comparing two trees by MP3
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_rf_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_rf.py`
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Comparing two trees by Robinson-Foulds
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.. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_tpted_thumb.png
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:ref:`sphx_glr_auto_examples_comparison_compute_tpted.py`
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Comparing two trees by TPTED
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Assessment
^^^^^^^^^^
Below is a gallery of examples for assessing the inferred phylogenetic tree using
functions in :mod:`scphylo.tl`.
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.. image:: /auto_examples/visualization/images/thumb/sphx_glr_plot_clonal_thumb.png
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:ref:`sphx_glr_auto_examples_visualization_plot_clonal.py`
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Visualizing a tree in clonal format
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.. image:: /auto_examples/visualization/images/thumb/sphx_glr_plot_dendrogram_thumb.png
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:ref:`sphx_glr_auto_examples_visualization_plot_dendrogram.py`
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Visualizing a tree in dendrogram format
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.. toctree::
:hidden:
:includehidden:
/auto_examples/reconstruction/index.rst
/auto_examples/comparison/index.rst
/auto_examples/assessment/index.rst
/auto_examples/visualization/index.rst
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.. rst-class:: sphx-glr-signature
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