[](https://www.tbi.univie.ac.at/RNA/#download)
[](https://github.com/ViennaRNA/ViennaRNA/actions)
[](https://github.com/ViennaRNA/ViennaRNA/releases)
[](https://anaconda.org/bioconda/viennarna)
[](https://anaconda.org/bioconda/viennarna)
[](https://aur.archlinux.org/packages/viennarna/)
# ViennaRNA Package
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 interactions between multiple RNA molecules
The package includes `Perl 5` and `Python` modules that give access to almost
all functions of the C library from within the respective scripting languages.
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).
See the [NEWS][file_news] and [CHANGELOG.md][file_changelog] files for changes between versions.
----
## Availability
The most recent source code should always be available through the
[official ViennaRNA website][vrna_website] and through
[github][vrna_github].
----
## Documentation
Executable programs shipped with the ViennaRNA Package are documented by
corresponding man pages, use e.g.:
```
man RNAfold
```
in a UNIX terminal to obtain the documentation for the `RNAfold` program.
HTML translations of all man pages can be found at [our official homepage][vrna_website_manpages].
We maintain a reference manual describing the `RNAlib` API that is automatically
generated with [doxygen][doxygen_website]. The HTML version of this reference
manual is available at [our official website][vrna_refman_website] and at
[ReadTheDocs][vrna_rtfm].
----
## Installation
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][file_install] for a more detailed description of the build
and installation process.*
### Quick Start
Usually you'll simply unpack the distribution tarball, configure and make:
```
tar -zxvf ViennaRNA-2.7.0.tar.gz
cd ViennaRNA-2.7.0
./configure
make
sudo make install
```
### User-dir Installation
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.
Use the `--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 `username`.
*Note, that the actual install destination paths are listed at the end
of the `./configure` output.*
### 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 `./configure`
script:
1. Unpack the `libsvm` archive to allow for SVM Z-score regression with the
program `RNALfold`:
```
cd src
tar -xzf libsvm-3.35.tar.gz
cd ..
```
2. Unpack the `dlib` archive to allow for concentration dependency computations with the
program `RNAmultifold`:
```
cd src
tar -xjf dlib-19.24.tar.bz2
cd ..
```
3. Install the autotools toolchain and the additional maintainer tools
`gengetopt`, `help2man`,`flex`,`xxd`, and `swig` if necessary. For
instance, in Debian based distributions, the following packages need
to be installed:
- `build-essential` (basic build tools, such as compiler, linker, etc.)
- `autoconf`, `automake`, `libtool`, `pkg-config` (autotools toolchain)
- `gengetopt` (to generate command line parameter parsers)
- `help2man` (to generate the man pages)
- `bison` and `flex`` (to generate sources for RNAforester)
- `vim-common` (for the `xxd` program)
- `swig` (to generate the scripting language interfaces)
- `liblapacke` (for `RNAxplorer`)
- `liblapack` (for `RNAxplorer`)
- A fortran compiler, e.g. `gfortran` (for `RNAxplorer`)
4. Finally, run the autoconf/automake toolchain:
```
autoreconf -i
```
After that, you can compile and install the ViennaRNA Package as if obtained
from the distribution tarball.
### Binary packages
Binary packages for several Linux-based platforms, Microsoft Windows, and
Mac OS X are available at [our official website][vrna_website_packages].
### Bioconda
Installation is also possible through [bioconda][bioconda_website].
After successfully setting up the bioconda channels
```
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
```
you can install the [viennarna bioconda package][vrna_bioconda_website]
through
```
conda install viennarna
```
### Python interface only
The Python 3 interface for the ViennaRNA Package library is
[available at PyPI][vrna_pypi_website] and can
be installed independently using Python's `pip`:
```
python -m pip install viennarna
```
#### Building a Python 3 sdist or wheel package
Our source tree allows for building/installing the Python 3
interface separately. For that, we provide the necessary packaging
files `pyproject.toml`, `setup.cfg`, `setup.py` and `MANIFEST.in`.
These files are created by our `autoconf` toolchain after a run
of `./configure`. Particular default compile-time features may be
(de-)activated by setting the corresponding boolean flags in
`setup.cfg`. See below for additional steps when building the
Python interface from a clean git clone.
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`.
#### Howto prepare the Python 3 sdist/wheel build from git repository
If you are about to create the Python interface from a fresh
clone of our git repository, you require additional steps after
running `./configure` as described above. In particular, some
autogenerated static files that are compiled into RNAlib must
be generated. To do so, run
```
cd src/ViennaRNA/static
make
cd ../../..
```
Additionally, if building the reference manual is not explicitly
turned off, the Python interface requires docstrings to be generated.
They are taken from the doxygen xml output which can be created by
```
cd doc
make refman-html
cd ..
```
Finally, the swig wrapper must be build using
```
cd interfaces/Python
make RNA/RNA.py
cd ../..
```
After these steps, the Python sdist and wheel packages can
be build as usual.
----
## References
If you use our software package, you may want to cite the follwing publications:
- [R. Lorenz et al. (2011)][vrna2_paper],
"ViennaRNA Package 2.0", Algorithms for Molecular Biology, 6:26
- [I.L. Hofacker (1994)][vrna_paper],
"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.*
----
## License
Please read the copyright notice in the file [COPYING][file_license]!
If you're a commercial user and find these programs useful, please consider
supporting further developments with a donation.
----
## Contact
We need your feedback! Send your comments, suggestions, and questions to
rna@tbi.univie.ac.at
Ivo Hofacker, Spring 2006
[file_news]: https://github.com/ViennaRNA/ViennaRNA/blob/master/NEWS
[file_changelog]: https://github.com/ViennaRNA/ViennaRNA/blob/master/CHANGELOG.md
[file_install]: https://github.com/ViennaRNA/ViennaRNA/blob/master/INSTALL
[file_license]: https://github.com/ViennaRNA/ViennaRNA/blob/master/COPYING
[file_param_rna2004]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_turner2004.par
[file_param_rna1999]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_turner1999.par
[file_param_dna2004]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/dna_mathews2004.par
[file_param_dna1999]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/dna_mathews1999.par
[file_param_andronescu2007]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_andronescou2007.par
[file_param_langdon2018]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_langdon2018.par
[file_param_inosine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_inosine_parameters.json
[file_param_pseudouridine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_pseudouridine_parameters.json
[file_param_m1Ψ]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_n1methylpseudouridine_parameters.json
[file_param_m5C]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_m5C_parameters.json
[file_param_m6A]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_m6A_parameters.json
[file_param_7DA]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_7DA_parameters.json
[file_param_purine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_purine_parameters.json
[file_param_dihydrouridine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_dihydrouridine_parameters.json
[vrna_website]: https://www.tbi.univie.ac.at/RNA
[vrna_github]: https://github.com/ViennaRNA/ViennaRNA
[vrna_website_manpages]: https://www.tbi.univie.ac.at/RNA/documentation.html#programs
[vrna_website_packages]: https://www.tbi.univie.ac.at/RNA/#binary_packages
[doxygen_website]: https://www.doxygen.nl
[vrna_refman_website]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman
[vrna_refman_epars]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/group__energy__parameters__rw.html
[vrna_refman_mod_base]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/group__modified__bases.html
[vrna_rtfm]: https://viennarna.readthedocs.io
[bioconda_website]: https://bioconda.github.io
[vrna_bioconda_website]: http://bioconda.github.io/recipes/viennarna/README.html
[vrna_pypi_website]: https://pypi.org/project/ViennaRNA
[vrna_refman_config]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/install.html#configuration
[vrna2_paper]: https://almob.biomedcentral.com/articles/10.1186/1748-7188-6-26
[vrna_paper]: https://link.springer.com/article/10.1007/BF00818163
[nndb_paper]: https://dx.doi.org/10.1093/nar/gkp892
[param2004_paper]: https://doi.org/10.1073/pnas.0401799101
Raw data
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"keywords": "synthetic, computational, biology, genetic, DNA, RNA, secondary, structure, prediction, minimum, free, energy, centroid, subopt, mfe, ViennaRNA, dynamic, partition function, modified base, constraints, programming",
"author": null,
"author_email": "Ronny Lorenz <ronny@tbi.univie.ac.at>, \"Ivo L. Hofacker\" <ivo@tbi.univie.ac.at>",
"download_url": "https://files.pythonhosted.org/packages/86/94/c65cfb4666efed90fc0fc241ee646054c5f1f7d16e83a39ab43ce7dfbe35/viennarna-2.7.0.tar.gz",
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"description": "[](https://www.tbi.univie.ac.at/RNA/#download)\n[](https://github.com/ViennaRNA/ViennaRNA/actions)\n[](https://github.com/ViennaRNA/ViennaRNA/releases)\n[](https://anaconda.org/bioconda/viennarna)\n[](https://anaconda.org/bioconda/viennarna)\n[](https://aur.archlinux.org/packages/viennarna/)\n\n# ViennaRNA Package\n\nA C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.\n\nAmongst other things, our implementations allow you to:\n\n- predict minimum free energy secondary structures\n- calculate the partition function for the ensemble of structures\n- compute various equilibrium probabilities\n- calculate suboptimal structures in a given energy range\n- compute local structures in long sequences\n- predict consensus secondary structures from a multiple sequence alignment\n- predict melting curves\n- search for sequences folding into a given structure\n- compare two secondary structures \n- predict interactions between multiple RNA molecules\n\nThe package includes `Perl 5` and `Python` modules that give access to almost\nall functions of the C library from within the respective scripting languages.\n\nThere is also a set of programs for analyzing sequence and distance\ndata using split decomposition, statistical geometry, and cluster methods.\nThey are not maintained any more and not built by default.\n\nThe code very rarely uses static arrays, and all programs should work for \nsequences up to a length of 32,700 (if you have huge amounts of memory that\nis).\n\nSee the [NEWS][file_news] and [CHANGELOG.md][file_changelog] files for changes between versions.\n\n----\n\n## Availability\n\nThe most recent source code should always be available through the\n[official ViennaRNA website][vrna_website] and through\n[github][vrna_github].\n\n----\n\n## Documentation\n\nExecutable programs shipped with the ViennaRNA Package are documented by\ncorresponding man pages, use e.g.:\n```\nman RNAfold\n```\nin a UNIX terminal to obtain the documentation for the `RNAfold` program.\nHTML translations of all man pages can be found at [our official homepage][vrna_website_manpages].\n\nWe maintain a reference manual describing the `RNAlib` API that is automatically\ngenerated with [doxygen][doxygen_website]. The HTML version of this reference\nmanual is available at [our official website][vrna_refman_website] and at\n[ReadTheDocs][vrna_rtfm].\n\n----\n\n## Installation\n\nFor best portability the ViennaRNA package uses the GNU autoconf and automake\ntools. The instructions below are for installing the ViennaRNA package from\nsource.\n\n*See the file [INSTALL][file_install] for a more detailed description of the build\nand installation process.*\n\n### Quick Start\n\nUsually you'll simply unpack the distribution tarball, configure and make:\n```\ntar -zxvf ViennaRNA-2.7.0.tar.gz\ncd ViennaRNA-2.7.0\n./configure\nmake\nsudo make install\n```\n\n### User-dir Installation\nIf you do not have root privileges on your computer, you might want to install\nthe ViennaRNA Package to a location where you actually have write access to.\nUse the `--prefix` option to set the installation prefix like so:\n```\n./configure --prefix=/home/username/ViennaRNA\nmake install\n```\n\nThis will install everything into a new directory `ViennaRNA` directly into\nthe home directory of user `username`.\n\n*Note, that the actual install destination paths are listed at the end\nof the `./configure` output.*\n\n### Install from git repository\n\nIf you attempt to build and install from our git repository, you need to\nperform some additional steps __before__ actually running the `./configure`\nscript:\n\n1. Unpack the `libsvm` archive to allow for SVM Z-score regression with the\n program `RNALfold`:\n```\ncd src\ntar -xzf libsvm-3.35.tar.gz\ncd ..\n```\n\n2. Unpack the `dlib` archive to allow for concentration dependency computations with the\n program `RNAmultifold`:\n```\ncd src\ntar -xjf dlib-19.24.tar.bz2\ncd ..\n```\n\n3. Install the autotools toolchain and the additional maintainer tools\n `gengetopt`, `help2man`,`flex`,`xxd`, and `swig` if necessary. For\n instance, in Debian based distributions, the following packages need\n to be installed:\n - `build-essential` (basic build tools, such as compiler, linker, etc.)\n - `autoconf`, `automake`, `libtool`, `pkg-config` (autotools toolchain)\n - `gengetopt` (to generate command line parameter parsers)\n - `help2man` (to generate the man pages) \n - `bison` and `flex`` (to generate sources for RNAforester)\n - `vim-common` (for the `xxd` program)\n - `swig` (to generate the scripting language interfaces)\n - `liblapacke` (for `RNAxplorer`)\n - `liblapack` (for `RNAxplorer`)\n - A fortran compiler, e.g. `gfortran` (for `RNAxplorer`)\n\n4. Finally, run the autoconf/automake toolchain:\n```\nautoreconf -i\n```\n\nAfter that, you can compile and install the ViennaRNA Package as if obtained\nfrom the distribution tarball.\n\n\n### Binary packages\nBinary packages for several Linux-based platforms, Microsoft Windows, and\nMac OS X are available at [our official website][vrna_website_packages].\n\n### Bioconda\nInstallation is also possible through [bioconda][bioconda_website].\nAfter successfully setting up the bioconda channels\n```\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\nconda config --set channel_priority strict\n```\nyou can install the [viennarna bioconda package][vrna_bioconda_website]\nthrough\n```\nconda install viennarna\n```\n\n\n### Python interface only\nThe Python 3 interface for the ViennaRNA Package library is\n[available at PyPI][vrna_pypi_website] and can\nbe installed independently using Python's `pip`:\n```\npython -m pip install viennarna\n```\n\n#### Building a Python 3 sdist or wheel package\nOur source tree allows for building/installing the Python 3\ninterface separately. For that, we provide the necessary packaging\nfiles `pyproject.toml`, `setup.cfg`, `setup.py` and `MANIFEST.in`.\n\nThese files are created by our `autoconf` toolchain after a run\nof `./configure`. Particular default compile-time features may be\n(de-)activated by setting the corresponding boolean flags in\n`setup.cfg`. See below for additional steps when building the\nPython interface from a clean git clone.\n\nRunning\n```\npython -m build\n```\nwill then create a source distribution (`sdist`) and a binary\npackage (`wheel`) in the `dist/` directory. These files can be\neasily installed via Python's `pip`.\n\n#### Howto prepare the Python 3 sdist/wheel build from git repository\nIf you are about to create the Python interface from a fresh\nclone of our git repository, you require additional steps after\nrunning `./configure` as described above. In particular, some\nautogenerated static files that are compiled into RNAlib must\nbe generated. To do so, run\n```\ncd src/ViennaRNA/static\nmake\ncd ../../..\n```\n\nAdditionally, if building the reference manual is not explicitly\nturned off, the Python interface requires docstrings to be generated.\nThey are taken from the doxygen xml output which can be created by\n```\ncd doc\nmake refman-html\ncd ..\n```\n\nFinally, the swig wrapper must be build using\n```\ncd interfaces/Python\nmake RNA/RNA.py\ncd ../..\n```\n\nAfter these steps, the Python sdist and wheel packages can\nbe build as usual.\n\n----\n\n## References\n\nIf you use our software package, you may want to cite the follwing publications:\n\n- [R. Lorenz et al. (2011)][vrna2_paper],\n\"ViennaRNA Package 2.0\", Algorithms for Molecular Biology, 6:26\n\n- [I.L. Hofacker (1994)][vrna_paper],\n\"Fast folding and comparison of RNA secondary structures\",\nMonatshefte fuer Chemie, Volume 125, Issue 2, pp 167-188\n\n\n*Note, that the individual executable programs state their own list of references\nin the corresponding man-pages.*\n\n----\n\n## License\n\nPlease read the copyright notice in the file [COPYING][file_license]!\n\nIf you're a commercial user and find these programs useful, please consider\nsupporting further developments with a donation.\n\n----\n\n## Contact\n\nWe need your feedback! Send your comments, suggestions, and questions to\nrna@tbi.univie.ac.at\n\nIvo Hofacker, Spring 2006\n\n\n[file_news]: https://github.com/ViennaRNA/ViennaRNA/blob/master/NEWS\n[file_changelog]: https://github.com/ViennaRNA/ViennaRNA/blob/master/CHANGELOG.md\n[file_install]: https://github.com/ViennaRNA/ViennaRNA/blob/master/INSTALL\n[file_license]: https://github.com/ViennaRNA/ViennaRNA/blob/master/COPYING\n[file_param_rna2004]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_turner2004.par\n[file_param_rna1999]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_turner1999.par\n[file_param_dna2004]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/dna_mathews2004.par\n[file_param_dna1999]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/dna_mathews1999.par\n[file_param_andronescu2007]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_andronescou2007.par\n[file_param_langdon2018]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_langdon2018.par\n[file_param_inosine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_inosine_parameters.json\n[file_param_pseudouridine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_pseudouridine_parameters.json\n[file_param_m1\u03a8]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_n1methylpseudouridine_parameters.json\n[file_param_m5C]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_m5C_parameters.json\n[file_param_m6A]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_m6A_parameters.json\n[file_param_7DA]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_7DA_parameters.json\n[file_param_purine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_purine_parameters.json\n[file_param_dihydrouridine]: https://github.com/ViennaRNA/ViennaRNA/blob/master/misc/rna_mod_dihydrouridine_parameters.json\n[vrna_website]: https://www.tbi.univie.ac.at/RNA\n[vrna_github]: https://github.com/ViennaRNA/ViennaRNA\n[vrna_website_manpages]: https://www.tbi.univie.ac.at/RNA/documentation.html#programs\n[vrna_website_packages]: https://www.tbi.univie.ac.at/RNA/#binary_packages\n[doxygen_website]: https://www.doxygen.nl\n[vrna_refman_website]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman\n[vrna_refman_epars]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/group__energy__parameters__rw.html\n[vrna_refman_mod_base]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/group__modified__bases.html\n[vrna_rtfm]: https://viennarna.readthedocs.io\n[bioconda_website]: https://bioconda.github.io\n[vrna_bioconda_website]: http://bioconda.github.io/recipes/viennarna/README.html\n[vrna_pypi_website]: https://pypi.org/project/ViennaRNA\n[vrna_refman_config]: https://www.tbi.univie.ac.at/RNA/ViennaRNA/refman/install.html#configuration\n[vrna2_paper]: https://almob.biomedcentral.com/articles/10.1186/1748-7188-6-26\n[vrna_paper]: https://link.springer.com/article/10.1007/BF00818163\n[nndb_paper]: https://dx.doi.org/10.1093/nar/gkp892\n[param2004_paper]: https://doi.org/10.1073/pnas.0401799101\n",
"bugtrack_url": null,
"license": "Disclaimer and Copyright The programs, library and source code of the Vienna RNA Package are free software. They are distributed in the hope that they will be useful but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Permission is granted for research, educational, and commercial use and modification so long as 1) the package and any derived works are not redistributed for any fee, other than media costs, 2) proper credit is given to the authors and the Institute for Theoretical Chemistry of the University of Vienna. If you want to include this software in a commercial product, please contact the authors. Note that the file ./src/ViennaRNA/plotting/naview.c has its own copyright attached. ",
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