.. augur documentation master file, created by
   sphinx-quickstart on Tue Apr 23 21:32:18 2019.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to augur's documentation!
=================================

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   quickstart
   tutorials
   commands
   APIdoc
   authors



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

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

=========================================================
Augur: A bioinformatics toolkit for phylogenetic analysis
=========================================================

    *One held to foretell events by omens.*
    (`Merriam-Webster <https://www.merriam-webster.com/dictionary/augur>`__)

Augur is a bioinformatics toolkit to track evolution from sequence and serological data.
It provides a collection of commands which are designed to be composable into larger processing pipelines.
Augur originated as part of `Nextstrain <https://nextstrain.org>`__, an open-source project to harness the scientific and public health potential of pathogen genome data.

.. toctree::
   :maxdepth: 2
   :caption: Table of contents

   installation
   quickstart
   tutorials
   commands
   APIdoc
   authors

Introduce augur on the doc home page
Docs: Introduce augur on the doc home page

This adapts content from the README.
