# ViennaRNA Package

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

A recent addition, RNAxplorer, requires lapacke (and thereby lapack
that depends on a version of blas). During configuration, the version
of blas that has been used for compiling lapack is searched for (see 
https://github.com/ViennaRNA/ViennaRNA/issues/206). An extra variable 
($BLAS) in the SlackBuild sets openblas as the version of blas used 
for lapack(e). Please, adjust  $BLAS to the blas used on your system.

An optional dependency is gri (see below), which is also on SBo.

A tutorial and other docs are available at:
https://viennarna.readthedocs.io/en/latest/

Examples and data can be found in /usr/share/ViennaRNA/

For those who wish to link the Vienna package to their own C, perl
or python programs (see below), the RNAlib Reference Manual can be
found at:
https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/api.html
https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/RNAlib-$VERSION.pdf
(or unpacked from the src: $PRGNAM-$VERSION/doc/RNAlib-$VERSION.pdf)

Amongst other things, the ViennRNA 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` and `Python 3` modules that give access
to almost all functions of the C library from within the respective
scripting languages.

The program RNA2fold can use gri (a language for scientific graphics 
programming) to create a colored postscript plot. 
(see https://viennarna.readthedocs.io/en/latest/tutorial/RNA2Dfold.html)