Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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ViennaRNA Package

The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding).

In case you are using our software for your publications you may want to cite:

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.
ViennaRNA Package 2.0
Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

News

04/13/2014

For a long time, Mac OS X users were not able to correctly build the Perl/Python interface of the ViennaRNA Package. Starting with v2.1.7, this limitation has been removed, and the interface should compile and work as expected. Please see the Install Notes for Mac OS X users for further details.

01/25/2013

Since ViennaRNA Package Version 2.1.0 we have enabled G-Quadruplex prediction support into RNAfold, RNAcofold, RNALfold, RNAalifold, RNAeval and RNAplot. See the changelog for details.

05/21/2012

A preliminary version of the ViennaRNA Package implementing RNA/DNA hybrid support can be found here

08/01/2011

With the new release of version 2, we introduce the most recent nearest neighbor energy model for all free energy calculations. Additionally, most of the stand-alone programs included are now able to read FASTA formatted input data. This makes conversion of you data files, as necessary in previous releases, obsolete!

Download the latest ViennaRNA Package

The latest stable release is Version 2.1.8 from August, 18th 2014

Select your required Package format below

Compile from Source Code

Installing from sourcecode is the recommended way to get most out of the ViennaRNA Package. For best portability the ViennaRNA package uses the GNU autoconf and automake tools and can thus be compiled and installed on almost every computer platform. See the INSTALL instructions for details.

ViennaRNA Package v2.1.8 (tar.gz, SourceCode) [5.3MB]

Install Fedora Core 19 binary RPM package

We provide precompiled binary RPM packages for users of Fedora Core 19.

ViennaRNA Package v2.1.8 (rpm, Fedora Core 19, 64bit) [5.7MB]
ViennaRNA Package v2.1.8 (rpm, Fedora Core 19, 32bit) [4.7MB]

In case you need the ViennaRNA Package for another version of Fedora please download the SourceCode Package. Then you can either install it as recommended or you can create your own RPM binary archive. For the latter case use the Fedora SPEC file to create a Fedora RPM via the regular RPM package build procedure.

Install viennarna2 package from AUR in ArchLinux

Installing the ViennaRNA Package on ArchLinux is quite easy. Just download the Arch Linux Source Package

ViennaRNA Package v2.1.8 (tar.gz, ArchLinux Source Package) [1.1k]

and proceed with the following steps:

  1. Extract the downloaded tarball with
    $ tar xzf viennarna2.tar.gz
    
  2. Run makepkg in the directory you just created.
    $ makepkg -s
    
    This downloads the code, compiles and packs it for pacman
  3. Install the package with pacman:
    $ pacman -U /path/to/pkg.tar.xz
    

Alternatively, you can also use an AUR repository tool like yaourt to install it directly from AUR::

$ yaourt -S viennarna2

Install Debian GNU/Linux binary package

We also provide precompiled binary packages for Debian GNU/Linux.

ViennaRNA Package v2.1.7 (deb, Debian/Ubuntu, 64bit) [3.5MB]
ViennaRNA Package v2.1.7 (deb, Debian/Ubuntu, 32bit) [8.1MB]
ViennaRNA Package v2.1.6 (deb, Debian, 32bit ARM/soft-float) [8.6MB]

Install Ubuntu package from PPA

The most convenient way to keep up-to-date with the latest ViennaRNA Packge is to use Ubuntu PPA:

sudo apt-add-repository ppa:j-4/vienna-rna
sudo apt-get update
sudo apt-get install vienna-rna

alternatively, our Debian GNU/Linux files should also work well with Ubuntu.

ViennaRNA Package v2.1.7 (deb, Debian/Ubuntu, 64bit) [3.5MB]
ViennaRNA Package v2.1.7 (deb, Debian/Ubuntu, 32bit) [8.1MB]
ViennaRNA Package v2.1.6 (deb, Raspbian, 32bit ARM/soft-float) [8.6MB]

Install for Windows with out Installer binary

We also provide an Installer program that installs the executable programs of the ViennaRNA Package for Microsoft Windows ©

ViennaRNA Package v2.1.7 (exe, Windows, 32bit) [9.3MB]
ViennaRNA Package v2.1.7 (exe, Windows, 64biet) [10MB]

The installer will not change the PATH variable of your system. In order to omit the path to the binaries while using the programs of the ViennaRNA Package, please add the path of your ViennaRNA Package installation directory to your PATH variable.

Other Packages:

Here we list all versions of the ViennaRNA Package that contain special features which have not been included into the main release yet:

ViennaRNA Package v2.1.6h (preliminary version implementing RNA/DNA hybrid support)

Older Versions:

There should rarely be a good reason to use any but the latest version of our software. However if you want to look up the old bugs, here's a list with most of the older releases for download:

2.1.x

ViennaRNA Package v2.1.7 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.6 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.5 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.4 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.3 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.2 (tar.gz, SourceCode) [5.2MB]
ViennaRNA Package v2.1.1 (tar.gz, SourceCode) [5.1MB]
ViennaRNA Package v2.1.0 (tar.gz, SourceCode) [5.1MB]

2.0.x

ViennaRNA Package v2.0.7 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.6 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.5 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.4 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.3b (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.3 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.2 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.1 (tar.gz, SourceCode) [3.8MB]
ViennaRNA Package v2.0.0 (tar.gz, SourceCode) [3.8MB]

1.8.x

ViennaRNA Package v1.8.5 (tar.gz, SourceCode) [1.3MB]
ViennaRNA Package v1.8.4 (tar.gz, SourceCode) [1.4MB]
ViennaRNA Package v1.8.3 (tar.gz, SourceCode) [1.4MB]
ViennaRNA Package v1.8.2 (tar.gz, SourceCode) [1.3MB]
ViennaRNA Package v1.8.1 (tar.gz, SourceCode) [1.3MB]
ViennaRNA Package v1.8.0 (tar.gz, SourceCode) [1.3MB]

1.7.x

ViennaRNA Package v1.7.2 (tar.gz, SourceCode) [1.3MB]
ViennaRNA Package v1.7.1 (tar.gz, SourceCode) [1.3MB]
ViennaRNA Package v1.7.0 (tar.gz, SourceCode) [1.2MB]

1.6.x

ViennaRNA Package v1.6.5 (tar.gz, SourceCode) [1.2MB]
ViennaRNA Package v1.6.4 (tar.gz, SourceCode) [1.4MB]
ViennaRNA Package v1.6.3 (tar.gz, SourceCode) [1.2MB]
ViennaRNA Package v1.6.2 (tar.gz, SourceCode) [1.2MB]
ViennaRNA Package v1.6.1 (tar.gz, SourceCode) [1.2MB]
ViennaRNA Package v1.6.0 (tar.gz, SourceCode) [1.2MB]
ViennaRNA Package v1.6alpha (tar.gz, SourceCode) [1.4MB]

1.5.x

ViennaRNA Package v1.5beta (tar.gz, SourceCode) [626kB]
ViennaRNA Package v1.5alpha (tar.gz, SourceCode) [533kB]

1.4.x

ViennaRNA Package v1.4 (tar.gz, SourceCode) [472kB]

1.3.x

ViennaRNA Package v1.3.1 (tar.gz, SourceCode) [270kB]
ViennaRNA Package v1.3 (tar.gz, SourceCode) [270kB]

1.2.x

ViennaRNA Package v1.2.1 (tar.gz, SourceCode) [214kB]
ViennaRNA Package v1.2 (tar.gz, SourceCode) [214kB]

1.1.x

ViennaRNA Package v1.1b (tar.gz, SourceCode) [193kB]