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+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
+
git://source.jalview.org / jabaws.git / blobdiff