This is Version 1.6 of the Vienna RNA Package.

The Vienna RNA packages consists of a few stand alone programs and a library that you can link your own programs with. The package allows you to

• predict minimum free energy secondary structures
• calculate the partition function for the ensemble of structures
• calculate suboptimal structures in a given energy range
• predict consensus secondary sctructures from a multiple sequence alignment
• scan large (genomic) sequences for stable local structures
• predict hybrid structures of two sequences
• predict melting curves
• search for sequences folding into a given structure
• compare RNA secondary structures and sequences

The package includes a Perl5 module that gives access to almost all functions of the C library from Perl.

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

Please read the copyright notice in the file COPYING!

The package should be easily portable. It is known to compile without modifications at least under
SunOS 5.x, IRIX 5.x and 6.x, various linux distributions, and windows with the CygWin environment. Other UNIX flavours, as well as Mac OS X should i present no problems.
You need a compiler that understands ANSI C. See the INSTALL file for details.

The following executables are provided:

RNAfold         predict secondary structures
RNAsubopt       calulate suboptimal structures in a given energy range
RNAalifold      predict a consensus structure for a set of aligned sequences
RNAcofold       calculate the hybrid structure of two RNA molecules
RNAduplex       predict possible hybridization sites for two RNAs
RNAeval         evaluate energy for given sequence and structure
RNALfold        calculate locally stable RNA secondary structures
RNAplfold       pair probabilities of local structures
RNAheat         calculate melting curves
RNAdistance     compare secondary structures
RNApdist        compare ensembles of secondary structures
RNApaln         alignment of RNA sequences with predicted pair propensities
RNAinverse      find sequences folding into given structures
RNAplot         draw RNA structures in PostScript, CVG, or GML
AnalyseDists    distance based phylogenies (neighbor joining, splits,...)
AnalyseSeqs     analyse sequence data

A couple of useful utililities can be found in the Utils directory.

All executables read from stdin and write to stdout and use command line switches rather than menus to be easily usable in pipes.

For more detailed information see the man pages.

We have included a patched version of D.G. Gilbert's readseq program for those who often process sequence files from databanks. See the the documentation in that directory for details.

Versions since 1.4 feature new energy parameters as described in Mathews et.al, JMB, 1999. For backward compatibility a parameter file with the version 1.3 parameter set (as described in Walter et.al (1994)) can be found in the file vienna13.par. The standard energy set is compiled in, but can also be found in the file default.par. Note that only free energies at 37C are new. Temperature dependencies are still derived from the old parameter set.
The code very rarely uses static arrays, and all programs should work for sequences up to at least 32700 nt (if you have huge amounts of memory that is).

If you're a commercial user and find these programs useful, please consider supporting further developments with a donation.

The most recent source code and documentation should always be available on the web at
http://www.tbi.univie.ac.at/~ivo/RNA/

We need your feedback! Send your comments, suggestions, and questions to rna@tbi.univie.ac.at

Ivo Hofacker