# How to cite the ViennaRNA Package

If you use our software and implemented algorithms for your scientific work, you might want to cite the corresponding publications.

## Main References

The overarching main publications for the ViennaRNA Package are:

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

- I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly, 125(2):167–188, 1994. URL: https://www.academia.edu/download/48689421/Fast_Folding_and_Comparison_of_RNA_Secon20160908-13624-1yg70az.pdf.

## Particular Algorithms and Features

To reference particular algorithms used in our sofware, you might want to consider citing the following publications:

### Consensus structure prediction

- I.L. Hofacker, M. Fekete, and P.F. Stadler. Secondary structure prediction for aligned RNA sequences. Journal of molecular biology, 319(5):1059–1066, 2002. doi:10.1016/S0022-2836(02)00308-X.

- S.H. Bernhart, I.L. Hofacker, S. Will, A.R. Gruber, and P.F. Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC bioinformatics, 9(1):474, 2008. doi:10.1186/1471-2105-9-474.

### Local pair probabilitiy and accessibility

- Stephan H Bernhart, Ivo L Hofacker, and Peter F Stadler. Local RNA base pairing probabilities in large sequences. Bioinformatics, 22(5):614–615, 2005. doi:10.1093/bioinformatics/btk014.

- Stephan H Bernhart, Ullrike Mückstein, and Ivo L Hofacker. RNA accessibility in cubic time. Algorithms for Molecular Biology, 6(1):3, 2011. doi:10.1186/1748-7188-6-3.

### Suboptimal secondary structures

- S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers, 49(2):145–165, February 1999. doi:10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G.

### k,l - Neighborhood

- Ronny Lorenz, Christoph Flamm, and Ivo L. Hofacker. 2d projections of RNA folding landscapes. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter F. Stadler, editors, German Conference on Bioinformatics 2009, volume 157 of Lecture Notes in Informatics, 11–20. Bonn, September 2009. Gesellschaft f. Informatik. URL: https://dl.gi.de/items/8f88acfe-c389-4dfe-b975-84a638900683.

### Experimental RNA structure probing

- Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, and Michael T. Wolfinger. Shape directed rna folding. Bioinformatics, 32(1):145–147, 2016. doi:10.1093/bioinformatics/btv523.

### Structure Constraints

- Ronny Lorenz, Ivo L. Hofacker, and Peter F. Stadler. RNA folding with hard and soft constraints. Algorithms for Molecular Biology, 11(1):1–13, 2016. doi:10.1186/s13015-016-0070-z.

### Non-redundant Boltzmann sampling

- Juraj Michálik, Hélène Touzet, and Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinformatics, 33(14):i283–i292, 2017. doi:10.1093/bioinformatics/btx269.