# ViennaRNA Package

A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Amongst other things, our implementations allow you to:

- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- compute various equilibrium probabilities
- calculate suboptimal structures in a given energy range
- compute local structures in long sequences
- predict consensus secondary structures from a multiple sequence alignment
- predict melting curves
- search for sequences folding into a given structure
- compare two secondary structures 
- predict hybridization structures of two RNA molecules

The package includes `Perl 5`, `Python 2`, and `Python 3` modules that give
access to almost all functions of the C library from within the respective
scripting languages.

There is also a set of programs for analyzing sequence and distance
data using split decomposition, statistical geometry, and cluster methods.
They are not maintained any more and not built by default.

The code very rarely uses static arrays, and all programs should work for 
sequences up to a length of 32,700 (if you have huge amounts of memory that
is).

For those who wish to link the Vienna package their own C, perl or python programs,
the RNAlib Reference Manual can be assessed at:

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html

or downloaded from:

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf

For further info see:

https://www.tbi.univie.ac.at/RNA/documentation.html