Ziplign documentation
=====================

Ziplign is a free application to visualise the comparison of two bacterial genomes.
It is intended to be easy to use: you just need to drag and drop two sequence
files to compare.
Ziplign will run BLAST for you and show you the results. There is no need to use a
terminal or type any commands.

.. image:: pics/zl_docs_overview_screenshots.gif
   :width: 70%
   :alt: screenshots showing an overview of ziplign

The source code is in the  `Ziplign GitHub repository <https://github.com/martinghunt/ziplign>`_,
under the permissive MIT license. Please report any issues on GitHub.

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

   installation
   loading
   viewing
   searching
   contig_editing
   saving_n_loading
   keyboard_shortcuts
   settings
   data_folder
   uninstalling
   contributing
   background
   faq