A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
Amongst other things, our 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
Python 2, and
Python 3 modules that give
access to almost all functions of the C library from within the respective
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).
Table of Contents
- Executable Programs
- Energy Parameters
For best portability the ViennaRNA package uses the GNU autoconf and automake tools. The instructions below are for installing the ViennaRNA package from source.
See the file INSTALL for a more detailed description of the build and installation process.
Usually you'll simply unpack the distribution tarball, configure and make:
tar -zxvf ViennaRNA-2.4.17.tar.gz cd ViennaRNA-2.4.17 ./configure make sudo make install
If you do not have root privileges on your computer, you might want to install
the ViennaRNA Package to a location where you actually have write access to.
--prefix option to set the installation prefix like so:
./configure --prefix=/home/username/ViennaRNA make install
This will install everything into a new directory
ViennaRNA directly into
the home directory of user
Note, that the actual install destination paths are listed at the end
Install from git repository
If you attempt to build and install from our git repository, you need to
perform some additional steps before actually running the
- Unpack the
libsvmarchive to allow for SVM Z-score regression with the program
cd src tar -xzf libsvm-3.24.tar.gz cd ..
Install the additional maintainer tools
swigif necessary. For instance, in RedHat based distributions, the following packages need to be installed:
gengetopt(to generate command line parameter parsers)
help2man(to generate the man pages)
flex-devel(to generate sources for RNAforester)
swig(to generate the scripting language interfaces)
Finally, run the autoconf/automake toolchain:
After that, you can compile and install the ViennaRNA Package as if obtained from the distribution tarball.
This release includes the
programs, which can also be obtained as independent packages. Running
./configure in the ViennaRNA directory will configure these packages as well.
However, for detailed information and compile time options, see the README and
INSTALL files in the respective subdirectories.
AnalyseDists offer some cluster analysis tools
(split decomposition, statistical geometry, neighbor joining, Ward's method) for
sequences and distance data. To also build these programs add
to your configure options.
kinfold program can be used to simulate the folding dynamics of an RNA
molecule, and is compiled by default. Use the
--without-kinfold option to
skip compilation and installation of Kinfold.
RNAforester program is used for comparing secondary structures using tree
alignment. Similar to Kinfold, use the
--without-forester option to skip
compilation and installation of RNAforester.
kinwalker algorithm performs co-transcriptional folding of RNAs, starting
at a user specified structure (default: open chain) and ending at the minimum
free energy structure. Compilation and installation of this program is
deactivated by default. Use the
--with-kinwalker option to enable building and
installation of Kinwalker.
RNAlocmin program is part of the
Basin Hopping Graph Framework and reads
secondary structures and searches for local minima by performing a gradient walk
from each of those structures. It then outputs an energetically sorted list of
local minima with their energies and number of hits to particular minimum, which
corresponds to a size of a gradient basin. Additional output consists of barrier
trees and Arhenius rates to compute various kinetic aspects. Compilation and
installation of this program is activated by default. Use the
--without-rnalocmin option to disable building and installation of RNAlocmin.
The ViennaRNA Package comes with scripting language interfaces for
Python 2, and
Python 3 (provided by
swig), that allow one to use the
implemented algorithms directly without the need of calling an executable
program. The necessary requirements are determined at configure time and
particular languages may be deactivated automatically, if the requirements are
not met. You may also switch-off particular languages by passing the
./configure --without-perl --without-python
will turn-off the
Perl 5 and
Python 2 interfaces.
Disabling the entire scripting language support alltogether can be accomplished
Streaming SIMD Extension support
Our latest version contains code that implements a faster multibranch loop
decomposition in global MFE predictions, as used e.g. in
implementation makes use of modern processors capability to execute particular
instructions on multiple data simultaneously (SIMD - single instruction multiple
data, thanks to W. B. Langdon for providing the modified code). Consequently,
the time required to assess the minimum of all multibranch loop decompositions
is reduced up to about one half compared to the runtime of the original
implementation. This feature is enabled by default since version 2.4.11 and a
dispatcher ensures that the correct implementation will be selected at runtime.
If for any reason you want to disable this feature at compile-time use the
following configure flag
Link Time Optimization (LTO)
To increase the performance of our implementations, the ViennaRNA Package tries to make use of the Link Time Optimization (LTO) feature of modern C-compilers. If you are experiencing any troubles at make-time or run-time, or the configure script for some reason detects that your compiler supports this feature although it doesn't, you can deactivate it using the flag
To enable concurrent computation of our implementations and in some cases parallelization of the algorithms we make use of the OpenMP API. This interface is well understood by most modern compilers. However, in some cases it might be necessary to deactivate OpenMP support and therefore transform RNAlib into a C-library that is not entirely thread-safe. To do so, add the following configure option
POSIX threads (pthread) support
To enable concurrent computation of multiple input data in
RNAalifold, and for our implementation of the concurrent
unordered insert, ordered output flush data structure
vrna_ostream_t we make
use of POSIX threads. This should be supported on all modern platforms and
usually does not pose any problems. In case you want to compile without POSIX
threads support for any reason, add the following configure option
SVM Z-score filter in RNALfold
RNALfold that comes with the ViennaRNA Package allows for z-score
filtering of its predicted results using a support vector machine (SVM).
However, the library we use to implement this feature (
libsvm) is statically
linked to our own RNAlib. If this introduces any problems for your own
third-party programs that link against RNAlib, you can safely switch off the
z-scoring implementation using
GNU Scientific Library
The new program
RNApvmin computes a pseudo-energy pertubation vector that aims
to minimize the discrepancy of predicted, and observed pairing probabilities.
For that purpose it implements several methods to solve the optimization
problem. Many of them are provided by the GNU Scientific Library, which is why
RNApvmin program, and the RNAlib C-library are required to be linked
libgsl. If this introduces any problems in your own third-party
programs that link against RNAlib, you can turn off a larger protion of
available minimizers in
RNApvmin and linking against
using the switch
For a complete list of all
./configure options and important environment
The ViennaRNA Package includes the following executable programs:
||Compute MFE structure, partition function and representative sample structures of k,l neighborhoods|
||Predict conserved RNA-RNA interactions between two alignments|
||Calculate secondary structures for a set of aligned RNA sequences|
||Calculate secondary structures of two RNAs with dimerization|
||Calculate distances between RNA secondary structures|
||Compute the density of states for the conformation space of a given RNA sequence|
||Compute the structure upon hybridization of two RNA strands|
||Evaluate free energy of RNA sequences with given secondary structure|
||Calculate minimum free energy secondary structures and partition function of RNAs|
||Calculate the specific heat (melting curve) of an RNA sequence|
||Find RNA sequences with given secondary structure (sequence design)|
||Calculate locally stable secondary structures for a set of aligned RNAs|
||Calculate locally stable secondary structures of long RNAs|
||RNA alignment based on sequence base pairing propensities|
||Calculate distances between thermodynamic RNA secondary structures ensembles|
||Convert energy parameter files from ViennaRNA 1.8 to 2.0 format|
||Predict RNA secondary structures including pseudoknots|
||Find targets of a query RNA|
||Calculate average pair probabilities for locally stable secondary structures|
||Draw RNA Secondary Structures in PostScript, SVG, or GML|
||Calculate a perturbation vector that minimizes discripancies between predicted and observed pairing probabilities|
||Find targets of a query H/ACA snoRNA|
||Calculate suboptimal secondary structures of RNAs|
||Calculate the thermodynamics of RNA-RNA interactions|
||Analyse sequence data|
||Analyse distance matrices|
A couple of useful utilities can be found in the src/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.
Together with this version we also distribute the programs
See the README files in the respective sub-directories.
If you use our software package, you may want to cite the follwing publications:
R. Lorenz et al. (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6:26
I.L. Hofacker (1994), "Fast folding and comparison of RNA secondary structures", Monatshefte fuer Chemie, Volume 125, Issue 2, pp 167-188
Note, that the individual executable programs state their own list of references in the corresponding man-pages.
Since version 2.0.0 the build-in energy parameters, also available as parameter file rna_turner2004.par, 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
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, a set of RNA energy parameters obtained by graft and grow genetic programming from Langdon et al. 2018, rna_langdon2018.par, and two sets of DNA parameters, dna_mathews1999.par and dna_mathews2004.par, are included in the package as well.
Please read the copyright notice in the file COPYING!
If you're a commercial user and find these programs useful, please consider supporting further developments with a donation.
We need your feedback! Send your comments, suggestions, and questions to firstname.lastname@example.org
Ivo Hofacker, Spring 2006