.. phylociraptor documentation master file, created by
   sphinx-quickstart on Thu Dec 17 14:15:04 2020.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. role:: raw-html(raw)
    :format: html


==========
Welcome to 
==========


.. image:: images/phylociraptor.png
   :width: 600px


:raw-html:`<br />` 

.. image:: https://img.shields.io/github/stars/reslp/phylociraptor?style=social
   :alt: githubstars
   :target: https://github.com/reslp/phylociraptor/

.. image:: https://img.shields.io/github/forks/reslp/phylociraptor?style=social
   :alt: githubforks
   :target: https://github.com/reslp/phylociraptor/

.. image:: https://img.shields.io/github/commit-activity/w/reslp/phylociraptor
   :alt: commits
   :target: https://github.com/reslp/phylociraptor/


Phylociraptor is a bioinformatics pipeline to create phylogenomic trees. It is easy to install, scalable, reproducable and fast and performs all steps of a typical phylogenomic analysis.


----------------------
Getting started
----------------------

* Read what phylociraptor can `do <introduction/about.html>`_ . 
* Learn how to obtain and install phylociraptor `here <introduction/installation.html>`_ .
* You can read the `quickstart <introduction/quickstart.html>`_ page to see how phylociraptor is run.
* To learn all about what phylociraptor does you can read your `in-depth <indepth/setup.html>`_ guide.


----------------------
Getting Help
---------------------- 

If you run into problems with phylociraptor please follow these steps:

1. Review the relevant parts of the manual.
2. Check the `known-issues <getting-help/problems.html>`_ page if your problems is already known.
3. Search the `issue tracker <https://github.com/reslp/phylociraptor/issues>`_ if other people are having the same problem.
4. Post an `issue <https://github.com/reslp/phylociraptor/issues>`_  on GitHub describing your problem.  


.. toctree::
   :caption: First steps
   :name: introduction
   :maxdepth: 1
   :hidden:

   introduction/about
   introduction/installation.rst
   introduction/quickstart
   introduction/minimal
   introduction/citation.rst

.. toctree::
   :caption: phylocirpator in-depth
   :name: indepth
   :maxdepth: 1
   :hidden:
   
   indepth/setup.rst
   indepth/config_files.rst
   indepth/indepth.rst
   indepth/output.rst
   indepth/util.rst
   indepth/add_tools.rst
   indepth/mltreeoptions.rst

.. toctree::
   :caption: Getting help
   :name: getting_help
   :maxdepth: 1
   :hidden:

   getting-help/problems.rst
   getting-help/faqs.rst
   getting-help/tips.rst
   getting-help/contact.rst