Get Started#

The ViennaRNA Package comes with a variety of executable programs and scripts as well as a C-library that provides access to our implemented algorithms. Moreover, the C-library is wrapped to scripting languages such as Perl 5 and Python.

Note

The latest stable release is Version 2.7.2

Installing from Source#

The instructions below are for installing the ViennaRNA package from source code.

Tip

Read the Customizing the Build Process section before you install our software if you intend to deviate from the default setup.

From release tarball

Usually you’ll just download the latest source tarball, unpack it and run configure and make:

tar -zxvf ViennaRNA-2.7.2.tar.gz
cd ViennaRNA-2.7.2
./configure
make
sudo make install

From Git repository

You can also get the latest source code from our git repository hosted at github:

git clone https://github.com/ViennaRNA/ViennaRNA.git

Documentation

Usually, there is no need to (re-)build the documentation, it is already part of the source code tarball! However, if you compile from a freshly cloned git repository or you’ve changed any of the source code, building the documentation is probably required.

To succeed with the compilation a few maintainer tools are required:

doxygen (to extract the API documentation)
sphinx-build (to compile the manual)
pdflatex (to compile a PDF version of the manual)
sphinx-multiproject
myst-parser
sphinx-copybutton
sphinxcontrib-bibtex
pydata-sphinx-theme
sphinx-design

If all the above tools are available, compilation of the documentation should succeed without any further problems

Python Package

Our source code allows for building a stand-alone Python interface. For that, we provide the necessary packaging files pyproject.toml, setup.cfg, setup.py and MANIFEST.in. They are created by our autoconf toolchain after a successful run of ./configure. Particular default compile-time features may be (de-)activated by setting the corresponding boolean flags in setup.cfg. Running

python -m build

will then create a source distribution (sdist) and a binary package (wheel) in the dist/ directory. These files can be easily installed via Python’s pip.

Customizing the Build Process#

The ViennaRNA Package includes additional executable programs such as

RNAforester,
Kinfold,
Kinwalker,
RNAlocmin, and
RNAxplorer.

Furthermore, we include several features in our C-library that may be activated by default, or have to be explicitly turned on at configure-time. Below we list a selection of the available configure options that affect the features included in all executable programs, the RNAlib C-library, and the corresponding scripting language interface(s).

Streaming SIMD Extension#

Since version 2.3.5 our sources contain code that implements a faster multibranch loop decomposition in global MFE predictions, as used e.g. in RNAfold. This implementation makes use of modern processors streaming SIMD extension (SSE) that provide the 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 --disable-simd

Scripting Language Interfaces#

The ViennaRNA Package comes with scripting language interfaces for Perl 5, Python (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 switch-off particular languages by passing the --without-perl and/or --without-python configure options, e.g.:

./configure --without-perl

will turn-off building the Perl 5 interface.

Tip

Disabling the scripting language support all-together can be accomplished using the following switch:

./configure --without-swig

Cluster Analysis#

The programs AnalyseSeqs and 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 --with-cluster to your configure options.

Kinfold#

The 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#

The 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#

The 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#

The 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.

RNAxplorer#

The RNAxplorer is a multitool, that offers different methods to explore RNA energy landscapes. In default mode it takes an RNA sequence as input and produces a sample of RNA secondary structures. The repellant sampling heuristic used in default mode iteratively penalizes base pairs of local minima of structures that have been seen too often. This results in a diverse sample set with the most important low free energy structures. Compilation and installation of this program is activated by default. Note, that this tool depends on the LAPACK library. Use the --without-rnaxplorer option to disable building and installation of RNAxplorer.

Link Time Optimization#

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:

./configure --disable-lto

Note, that gcc before version 5 is known to produce unreliable LTO code, especially in combination with SIMD. We therefore recommend using a more recent compiler (GCC 5 or above) or to turn off one of the two features, LTO or SIMD optimized code.

OpenMP#

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:

./configure --disable-openmp

POSIX threads#

To enable concurrent computation of multiple input data in RNAfold, and for our implementation of the concurrent unordered insert, ordered output flush data structure vrna_ostream_t we make use of POSIX threads (pthread). This should be supported on all modern platforms and usually does not pose any problems. Unfortunately, we use a threadpool implementation that is not compatible with Microsoft Windows yet. Thus, POSIX thread support can not be activated for Windows builds until we have fixed this problem. If you want to compile RNAfold and RNAlib without POSIX threads support for any other reasons, add the following configure option:

./configure --disable-pthreads

SVM Z-score filter#

By default, RNALfold that comes with the ViennaRNA Package allows for Z-score filtering of its predicted results using a Support Vector Machine (SVM) provided by the LIBSVM library. However, this library 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:

./configure --without-svm

GNU Scientific Library#

The program RNApvmin computes a pseudo-energy perturbation 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 (GSL), which is why the RNApvmin program, and the RNAlib C-library are required to be linked against libgsl. If this introduces any problems in your own third-party programs that link against RNAlib, you can turn off a larger portion of available minimizers in RNApvmin and linking against libgsl all-together, using:

./configure --without-gsl

Multiple-precision Floating-Point Computations#

Our Non-redundant Boltzmann Sampling implementation uses multi-precision floating-point computations provided by the GNU MPFR library by default. This requires linking against libmpfr and libgmp. You can switch off this feature using:

./configure --disable-mpfr

Universal binaries#

If you intend to build the ViennaRNA for Mac OS X such that it runs on both, x86_64 and the arm64 (Apple Silicon Processors) architectures, you need to build a so-called universal binary. Note, however, that to accomplish this task, you might need to deactivate any third-party library dependency as in most cases, only one architecture will be available at link time. This includes the Perl 5 and Python interfaces but might also concern also MPFR and GSL support, possibly even more. In order to compile and link the programs, library, and scripting language interfaces of the ViennaRNA Package for multiple architectures, we’ve added a new configure switch that sets up the required changes automatically:

./configure --enable-universal-binary

Note

With link time optimization turned on, MacOS X’s default compiler (llvm/clang) generates an intermediary binary format that can not easily be combined into a multi-architecture library. Therefore, the --enable-universal-binary switch turns off Link Time Optimization!

Disable C11/C++11 features#

By default, we use C11/C++11 features in our implementations. This mainly accounts for unnamed unions/structs within RNAlib. The configure script automatically detects whether or not your compiler understands these features. In case you are using an older compiler, these features will be deactivated by setting a specific pre-processor directive. If for some reason you want to deactivate C11/C++11 features despite the capabilities of your compiler, use the following configure option:

./configure --disable-c11

Deprecated symbols#

Since version 2.2 we are in the process of transforming the API of our RNAlib. Hence, several symbols are marked as deprecated whenever they have been replaced by the new API. By default, deprecation warnings at compile time are deactivated. If you want to get your terminal spammed by tons of deprecation warnings, enable them using:

./configure --enable-warn-deprecated

Single precision#

Calculation of partition functions (via RNAfold -p) uses double precision floats by default, to avoid overflow errors on longer sequences. If your machine has little memory and you don’t plan to fold sequences over 1,000 bases in length you can compile the package to do the computations in single precision by running:

./configure --enable-floatpf

Warning

Using this option is discouraged and not necessary on most modern computers.

Help#

For a complete list of all ./configure options and important environment variables, type:

./configure --help

For more general information on the build process see the INSTALL file.

Build your own Binary Package from SourceCode#

If you don’t find a precompiled package for your linux distribution, or in case you just want to create a binary package by yourself, have a look into the packaging/ directory of our source tarball. It includes a list of some configuration files that we use for package generation:

For RPM based distributions, we use this SPEC file, originally written for Fedora, but meanwhile extended to work for at least the Linux distributions we provide binary packages ourselves.
Our binary package for ArchLinux was generated using this PKGBUILD file, which is also part of the viennarna source package available through the ArchLinux User Repository (AUR).
The configuration files for our binary Debian and Ubuntu packages are included in the source tarball within the packaging/debian directory.
Finally, for our MacOS X package, we make use of the pkgbuild, productbuild, and hditool commandline tools. The corresponding configuration files are included in our tarball in the directory packaging/macosx. For simplicity, you can instruct the autotools toolchain to automatically build the installer disk image by adding the following configure switch:
```
./configure --enable-macosx-installer
```
This creates a file packaging/macosx/ViennaRNA-2.7.2-MacOSX.dmg.

Our binary packages in the above section are mainly build using the openSUSE Build Service, while the Windows Installer is created using the MinGW cross-compiler and the NSIS install system. The MacOS X installer is build on github via github actions.