Here, we give a brief introduction into the problems that can be addressed with RNAlib and how our implementations work in general

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►Getting Started
Installation and Configuration	A documentation on how to configure the different features of `RNAlib`, how to install the ViennaRNA Package, and finally, how to link you own programs against `RNAlib`
HelloWorld
HelloWorld (Perl/Python)
►Concepts and Algorithms
RNA Structure
Distance Measures
Free Energy of Secondary Structures	A description on how secondary structures are decomposed into individual loops to eventually evaluate their stability in terms of free energy
Secondary Structure Folding Grammar	A description of the basic grammar to generate secondary structures, used for almost all prediction algorithms in our library and how to modify it
RNA Secondary Structure Landscapes	A description of the implicit landscape-like network of structures that appears upon modelling the transition of one structure into another
Minimum Free Energy Algorithm(s)	Computing the Minimum Free Energy (MFE), i.e. the most stable conformation in thermodynamic equilibrium
Partition Function and Equilibrium Probabilitiy Algorithm(s)
Suboptimals and (other) Representative Structures
RNA-RNA Interaction
Locally Stable Secondary Structures
Comparative Structure Prediction
Classified DP variations
RNA Sequence Design
Experimental Structure Probing Data
Ligand Binding
(Tertiary) Structure Motifs
►I/O Formats
RNA Structure Notations
File Formats
Plotting
►Basic Data Structures
Sequence and Structure Data
The 'Fold Compound'
Model Details
►API Features
RNAlib API v3.0
Callback Functions
Scripting Language interface(s)
Additional Utilities
►Examples
C Examples
Perl5 Examples
Python Examples
Contributing to the ViennaRNA Package
Changelog
Deprecated List
Bug List
Bibliography