Update README.rst to README.md

README.rst

-=====================================================
-de Novo Ambiguous Restraints for Iterative Assignment
-=====================================================
+## de Novo Ambiguous Restraints for Iterative Assignment
 
 **A pipeline for automated de novo contact map assignment**
 
-.. image:: https://img.shields.io/readthedocs/pip.svg
-    :target: http://bis-aria.pages.pasteur.fr/ariaec
-    :alt: Read the Doc
-    
-.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg
-   :target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
-   :alt: Pipeline status
-
-.. image:: https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg
-   :target: https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master
-   :alt: Coverage report
-   
-.. image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg
-   :target: https://doi.org/10.1093/bioinformatics/btl589
-   :alt: DOI status
-
+[![pipeline status](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/pipeline.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
+[![coverage report](https://gitlab.pasteur.fr/bis-aria/ariaec/badges/master/coverage.svg)](https://gitlab.pasteur.fr/bis-aria/ariaec/commits/master)
+[![documentation](https://img.shields.io/readthedocs/pip.svg)](http://bis-aria.pages.pasteur.fr/ariaec)
+[![aria paper](https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtl589-blue.svg)](https://doi.org/10.1093/bioinformatics/btl589)
 
 **ariaec**  is a Python_ library that provides *de novo* structure prediction
 based on ARIA_ pipeline and evolutionary restraints inferred from co-evolution.
@@ -31,48 +17,29 @@ analyze contact maps or protein structures and generate statistics from a culled
 list of PDB files.
 
 
-Quick Start
------------
+## Quick Start
 
 Be sure to check if the following packages are correctly installed with
 your python installation or virtual environment.
 
-* **pip** (>= 9.0)
-* **setuptools** (>= 18.0)
-* **numpy** (>= 1.11)
-* **cns-solve** (1.21)
+- **pip** (>= 9.0)
+- **setuptools** (>= 18.0)
+- **numpy** (>= 1.11)
+- **cns-solve** (1.21)
 
 Then the easiest solution is to call the **pip** command below :
 
-   ``pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec``
+   `pip install git+https://gitlab.pasteur.fr/bis-aria/ariaec`
 
 For more information about installation and usage, please refer to the
-`ARIAEC documentation <http://bis-aria.pages.pasteur.fr/ariaec>`_.
-
-.. raw:: html
-
-    <div class="alert alert-warning">
-
+[ARIAEC documentation](http://bis-aria.pages.pasteur.fr/ariaec)
 
 This package contains patches for **CNS-solve** which needs to be compiled
 after the installation. Please follow post installation instruction
 before using ``aria2`` pipeline.
-
-.. raw:: html
-
-    </div>
+{: .alert .alert-warning .text-center}
     
-Contributing
-------------
+## Contributing
 
-Please read `guidelines for contributing <https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md>`_ for any
+Please read [guidelines for contributing](https://gitlab.pasteur.fr/bis-aria/ariaec/blob/master/CONTRIBUTING.md) for any
 suggestions or bug report.
-
-
-
-.. Hyperlinks
-.. _ZIP: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.zip
-.. _TAR: https://gitlab.pasteur.fr/bis-aria/ariaec/repository/master/archive.tar
-.. _Gitlab: https://gitlab.pasteur.fr/bis-aria/ariaec
-.. _ARIA: http://aria.pasteur.fr
-.. _Python: https://www.python.org