How to cite the ViennaRNA Package
=================================

If you use our software and implemented algorithms for your scientific work, you might
want to cite the corresponding publications.


Main References
---------------

The *overarching* main publications for the ViennaRNA Package are:

.. bibliography::
   :filter: tags % "vrna_main"
   :list: bullet


Particular Algorithms and Features
----------------------------------

To reference particular algorithms used in our sofware, you might want to consider citing
the following publications:

Consensus structure prediction
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: False
   :list: bullet

   hofacker:2002
   bernhart:2008


Local pair probabilitiy and accessibility
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: tags % "local_probs"
   :list: bullet


Suboptimal secondary structures
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: False
   :list: bullet

   wuchty:1999


k,l - Neighborhood
^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: False
   :list: bullet

   lorenz:2009


Experimental RNA structure probing
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: False
   :list: bullet

   lorenz:2016a


Structure Constraints
^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: False
   :list: bullet

   lorenz:2016b

Non-redundant Boltzmann sampling
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. bibliography::
   :filter: tags % "nonredundant"
   :list: bullet
