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========================
Welcome!
========================

This website serves as documentation to the Cassiopeia software suite, maintained by the `Yosef Lab
<https://yoseflab.github.io/>`_ at UC Berkeley.

Cassiopeia [Jones20]_ is a package for end-to-end phylogenetic reconstruction of single-cell lineage tracing data. The package is composed of four independent modules:

* ``preprocess`` for processing sequencing FASTQ data to character matrices
* ``solver`` for performing tree inference
* ``simulator`` for simulating trees and character-level data
* ``plotting`` for plotting trees.

If you find this useful for your research, please consider citing Cassiopeia [Jones20]_.

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                    <h5 class="card-title">Installation</h5>
                    <p class="card-text">New to <em>Cassiopeia</em>? Check out the installation guide.
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                    <h5 class="card-title">User guide</h5>
                    <p class="card-text">The tutorials provide in-depth information on running Cassiopeia.</p>

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                    <p class="card-text">Have a question or found a bug? File an issue.</p>

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    `File an issue <https://github.com/YosefLab/Cassiopeia/issues>`_

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