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\bibitem{bernhart:2008}
S.H. Bernhart, I.L. Hofacker, S.~Will, A.R. Gruber, and P.F. Stadler.
\newblock {RNAalifold}: Improved consensus structure prediction for {RNA}
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\newblock {\em BMC bioinformatics}, 9(1):474, 2008.

\bibitem{bernhart:2006}
S.H. Bernhart, H.~Tafer, U.~M{\"u}ckstein, C.~Flamm, P.F. Stadler, and I.L.
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\newblock Partition function and base pairing probabilities of {RNA}
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\newblock {\em Algorithms for Molecular Biology}, 1(1):3, 2006.

\bibitem{fontana:1993b}
W.~Fontana, P.F. Stadler, E.G. Bornberg-Bauer, T.~Griesmacher, I.L. Hofacker,
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\newblock {RNA} folding and combinatory landscapes.
\newblock {\em Physical review E}, 47(3):2083, 1993.

\bibitem{hofacker:2002}
I.L. Hofacker, M.~Fekete, and P.F. Stadler.
\newblock Secondary structure prediction for aligned {RNA} sequences.
\newblock {\em Journal of molecular biology}, 319(5):1059--1066, 2002.

\bibitem{hofacker:1994}
I.L. Hofacker, W.~Fontana, P.F. Stadler, L.S. Bonhoeffer, M.~Tacker, and
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\newblock Fast folding and comparison of {RNA} secondary structures.
\newblock {\em Monatshefte f{\"u}r Chemie/Chemical Monthly}, 125(2):167--188,
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\bibitem{hofacker:2006}
I.L. Hofacker and P.F. Stadler.
\newblock Memory efficient folding algorithms for circular {RNA} secondary
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\newblock {\em Bioinformatics}, 22(10):1172--1176, 2006.

\bibitem{lorenz:2011}
Ronny Lorenz, Stephan~H. Bernhart, Christian H{\"o}ner~zu Siederdissen, Hakim
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\newblock {ViennaRNA} package 2.0.
\newblock {\em Algorithms for Molecular Biology}, 6(1):26, 2011.

\bibitem{lorenz:2009}
Ronny Lorenz, Christoph Flamm, and Ivo~L. Hofacker.
\newblock 2d projections of {RNA} folding landscapes.
\newblock In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and
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  volume 157 of {\em Lecture Notes in Informatics}, pages 11--20, Bonn,
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\bibitem{mathews:2004}
D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M.~Zuker, and D.H.
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\newblock Incorporating chemical modification constraints into a dynamic
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\newblock {\em Proceedings of the National Academy of Sciences of the United
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\bibitem{mccaskill:1990}
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\newblock The equilibrium partition function and base pair binding
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\newblock {\em Biopolymers}, 29(6-7):1105--1119, 1990.

\bibitem{shapiro:1988}
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\newblock An algorithm for comparing multiple {RNA} secondary structures.
\newblock {\em Computer applications in the biosciences: CABIOS},
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\bibitem{turner:2010}
D.H. Turner and D.H. Mathews.
\newblock {NNDB}: The nearest neighbor parameter database for predicting
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\newblock {\em Nucleic Acids Research}, 38(suppl 1):D280--D282, 2010.

\bibitem{zuker:1981}
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\newblock Optimal computer folding of large {RNA} sequences using
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\newblock {\em Nucleic acids research}, 9(1):133--148, 1981.

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