RNAmutants is described in the following paper:

J. Waldispühl, S. Devadas, B. Berger and P. Clote,
Efficient Algorithms for Probing the RNA Mutation Landscape,
PLoS Computational Biology, August 8th, 2008.
[abstract] [bibtex-entry]

If you find this software useful for your research, please cite this paper. RNAmutants is based on previous works and algorithms published under:

P. Clote, J. Waldispühl, B. Behzadi and J.-M. Steyaert,
Energy landscape of k-point mutants of an RNA molecule,
[abstract] [bibtex-entry]
Bioinformatics Vol. 21, p. 4140-4147, 2005. doi:10.1093/bioinformatics/bti669

J. Waldispühl, B. Behzadi and J.-M. Steyaert,
An Approximate Matching Algorithm for Finding (Sub-)Optimal Sequences in S-attributed Grammars,
[abstract] [bibtex-entry]
Proc. ECCB 2002, Bioinformatics Vol. 18, p. 250-259, 2002.