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README

This is Version 1.6 of the Vienna RNA Package.
This is a pre-release possibly containing more bugs than usual!
------------------------------------------------
See the NEWS and Changelog files for differences to previous versions.

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
- predict melting curves
- search for sequences folding into a given structure
- compare two secondary structures 

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.

See the NEWS and Changelog files for changes between versions.

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, linux, and windows with the CygWin environment.
Other UN*X flavours should 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
RNAheat		calculate melting curves
RNAdistance	compare secondary structures
RNApdist	compare ensembles of secondary structures
RNAinverse	find sequences folding into given structures
AnalyseSeqs	analyse sequence data
AnalyseDists	analyse distance matrices

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 a length of 32700 (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, Autumn 2002

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