slackbuilds/academic/ViennaRNA/README

# ViennaRNA Package

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

A tutorial (see /usr/doc/$PRGNAM-$VERSION/RNA-tutorial-$VERSION.pdf)
and examples can be found in /usr/share/$PRGNAM/tutorial and
/usr/share/$PRGNAM/examples

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
assessed at:

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/index.html
(or unpacked from the src: $PRGNAM-$VERSION/doc/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 5` and `Python 3` modules that give access
to almost all functions of the C library from within the respective
scripting languages. For this reason, python3 is a dependency

The `Python 2` module can be built as well, or instead of the one
for `Python 3`; just edit the SlackBuild or run it by setting build
options PYTHON=yes PYTHON3=no.  (e.g. in sbopkg or run it from
the commandline -within the directory containing the SlackBuild
script and downloaded source archive- as: `PYTHON=yes PYTHON3=no
./ViennaRNA.SlackBuild`)

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 further info see:

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