This is Version 2.0.7 of the ViennaRNA Package.
------------------------------------------------
See the NEWS and Changelog files for differences to previous versions.

The ViennaRNA Package consists of a few stand alone programs and a 
library that you can link your own programs with. 
Together with this version we distribute the Kinfold and RNAforester
programs. See the README files in the respective sub-directories.

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

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.

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 UNIX flavors should present no problems.
You need a compiler that understands ANSI C. See the INSTALL file for details.

The following executables are provided:
RNA2Dfold       Compute MFE structure, partition function and representative sample structures of k,l neighborhoods
RNAaliduplex    Predict conserved RNA-RNA interactions between two alignments
RNAalifold      Calculate secondary structures for a set of aligned RNA sequences
RNAcofold       Calculate secondary structures of two RNAs with dimerization
RNAdistance     Calculate distances between RNA secondary structures
RNAduplex       Compute the structure upon hybridization of two RNA strands
RNAeval         Evaluate free energy of RNA sequences with given secondary structure
RNAfold         Calculate minimum free energy secondary structures and partition function of RNAs
RNAheat         Calculate the specific heat (melting curve) of an RNA sequence
RNAinverse      Find RNA sequences with given secondary structure (sequence design)
RNALalifold     Calculate locally stable secondary structures for a set of aligned RNAs
RNALfold        Calculate locally stable secondary structures of long RNAs
RNApaln         RNA alignment based on sequence base pairing propensities
RNApdist        Calculate distances between thermodynamic RNA secondary structures ensembles
RNAparconv      Convert energy parameter files from ViennaRNA 1.8 to 2.0 format
RNAPKplex       Predict RNA secondary structures including pseudoknots
RNAplex         Find targets of a query RNA
RNAplfold       Calculate average pair probabilities for locally stable secondary structures
RNAplot         Draw RNA Secondary Structures in PostScript, SVG, or GML
RNAsnoop        Find targets of a query H/ACA snoRNA
RNAsubopt       Calculate suboptimal secondary structures of RNAs
RNAup           Calculate the thermodynamics of RNA-RNA interactions 
AnalyseSeqs     Analyse sequence data
AnalyseDists    Analyse distance matrices

A couple of useful utilities 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. Perl utilities contain
POD documentation that can be read by typing e.g.
perldoc relplot.pl

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.

Since version 2.0 the build-in energy parameters (available as parameter
file default.par as well) are taken from:

D.H. Mathews et al. (2004),
"Incorporating chemical modification constraints into a dynamic programming
algorithm for prediction of RNA secondary structure",
Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292

and

D.H Turner et al. (2009), "NNDB: The nearest neighbor parameter database
for predicting stability of nucleic acid secondary structure",
Nucleic Acids Research: 38, pp 280-282

For backward compatibility we also provide energy parameters from Turner et al.
1999 in the file 'rna_turner1999.par'. Additionally, a set of trained RNA energy
parameters from Andronescou et al. 2007 'rna_andronescou2007.par' and two sets
of DNA parameters ('dna_mathews1999.par' and 'dna_mathews2004.par') are included
in the package as well.
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.a/~ivo/RNA

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

Ivo Hofacker, Spring 2006

