.. PhyloJunction documentation master file, created by
   sphinx-quickstart on Mon Aug  1 09:58:05 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

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PhyloJunction
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.. toctree::
   :maxdepth: 3
   :hidden:
   
   Home <self>
   Installation <installing.rst>
   Documentation <pjdoc/index.rst>

   Library API Reference <modules.rst>

|pj| (PJ) is a pure-|Python3| library designed as a framework for:

    (i) simulating evolutionary models;
    (ii) summarizing and visualizing simulated data;
    (iii) prototyping and testing new models;

In order to meet these goals, |pj| implements an extensible ecosystem of models and parsing functionalities that it exposes to users through command-line (CLI) and graphical user interfaces (GUI).

Interacting with the CLI and GUI normally involves specifying a model by entering commands written in the `phylojunction` (lowercase) scripting language.
After that, |pj| samples (i.e., simulates) values for each of the model variables, parses and summarizes those values, and outputs the result as text-formatted tables.
If interacting with the GUI, users can further inspect graphical summaries of those values.

On this website, you will find instructions and tutorials on how to :doc:`install <installing>` and use |pj|.
Please refer to the relevant sections in the :doc:`documentation <pjdoc/index>` for help with questions, bug reports, and feature requests.

.. Subroutines for building models, simulating data and parsing results are nonetheless functional outside of the standalone user interfaces, and can be accessed via custom scripts or from within the Python interpreter.

.. Indices and tables
.. ==================

.. * :ref:`genindex`
.. * :ref:`modindex`
.. * :ref:`search`