=======================
Concepts and Algorithms
=======================

Our library is grouped into several modules, each addressing different
aspects of RNA secondary structure related problems. This is an overview
of the concepts and algorithms for which implementations can be found
in this library.

Almost all of them rely on the physics based Nearest Neighbor Model
for RNA secondary structure prediction.

.. toctree::
   :maxdepth: 1
   :caption: Modules:

   eval
   grammar
   landscape
   mfe
   pf_fold
   subopt_and_representatives
   cofold
   class_fold
   inverse
   probing_data
   ligand_binding
   paired_modules
   modified_bases
   utils

.. toctree::
   :maxdepth: 1
   :caption: General Remarks:

   vrna_3.0
   callbacks
   deprecated
