
\begin{DoxyDescription}
\item[\label{_CITEREF_bernhart:2006}%
\mbox{[}1\mbox{]}]S.\-H. Bernhart, H.~Tafer, U.~M\"{u}ckstein, C.~Flamm, P.\-F. Stadler, and I.\-L. Hofacker. Partition function and base pairing probabilities of R\-N\-A heterodimers. {\itshape Algorithms for Molecular Biology}, 1(1)\-:3, 2006.


\item[\label{_CITEREF_bernhart:2008}%
\mbox{[}2\mbox{]}]S.\-H. Bernhart, I.\-L. Hofacker, S.~Will, A.\-R. Gruber, and P.\-F. Stadler. R\-N\-Aalifold\-: Improved consensus structure prediction for R\-N\-A alignments. {\itshape B\-M\-C bioinformatics}, 9(1)\-:474, 2008.


\item[\label{_CITEREF_fontana:1993b}%
\mbox{[}3\mbox{]}]W.~Fontana, P.\-F. Stadler, E.\-G. Bornberg-\/\-Bauer, T.~Griesmacher, I.\-L. Hofacker, M.~Tacker, P.~Tarazona, E.\-D. Weinberger, and P.~Schuster. R\-N\-A folding and combinatory landscapes. {\itshape Physical review E}, 47(3)\-:2083, 1993.


\item[\label{_CITEREF_hofacker:2006}%
\mbox{[}4\mbox{]}]I.\-L. Hofacker and P.\-F. Stadler. Memory efficient folding algorithms for circular R\-N\-A secondary structures. {\itshape Bioinformatics}, 22(10)\-:1172--1176, 2006.


\item[\label{_CITEREF_hofacker:1994}%
\mbox{[}5\mbox{]}]I.\-L. Hofacker, W.~Fontana, P.\-F. Stadler, L.\-S. Bonhoeffer, M.~Tacker, and P.~Schuster. Fast folding and comparison of R\-N\-A secondary structures. {\itshape Monatshefte f\"{u}r Chemie/\-Chemical Monthly}, 125(2)\-:167--188, 1994.


\item[\label{_CITEREF_hofacker:2002}%
\mbox{[}6\mbox{]}]I.\-L. Hofacker, M.~Fekete, and P.\-F. Stadler. Secondary structure prediction for aligned R\-N\-A sequences. {\itshape Journal of molecular biology}, 319(5)\-:1059--1066, 2002.


\item[\label{_CITEREF_lorenz:2009}%
\mbox{[}7\mbox{]}]Ronny Lorenz, Christoph Flamm, and Ivo~L. Hofacker. 2d projections of R\-N\-A folding landscapes. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter~F. Stadler, editors, {\itshape German Conference on Bioinformatics 2009}, volume 157 of {\itshape Lecture Notes in Informatics}, pages 11--20, Bonn, September 2009. Gesellschaft f. Informatik.


\item[\label{_CITEREF_lorenz:2011}%
\mbox{[}8\mbox{]}]Ronny Lorenz, Stephan~H. Bernhart, Christian H\"{o}ner~zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter~F. Stadler, and Ivo~L. Hofacker. Vienna\-R\-N\-A package 2.\-0. {\itshape Algorithms for Molecular Biology}, 6(1)\-:26, 2011. 


\item[\label{_CITEREF_mathews:2004}%
\mbox{[}9\mbox{]}]D.\-H. Mathews, M.\-D. Disney, J.\-L. Childs, S.\-J. Schroeder, M.~Zuker, and D.\-H. Turner. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of R\-N\-A secondary structure. {\itshape Proceedings of the National Academy of Sciences of the United States of America}, 101(19)\-:7287, 2004.


\item[\label{_CITEREF_mccaskill:1990}%
\mbox{[}10\mbox{]}]J.\-S. Mc\-Caskill. The equilibrium partition function and base pair binding probabilities for R\-N\-A secondary structure. {\itshape Biopolymers}, 29(6-\/7)\-:1105--1119, 1990.


\item[\label{_CITEREF_shapiro:1990}%
\mbox{[}11\mbox{]}]B.\-A. Shapiro and K.~Zhang. Comparing multiple R\-N\-A secondary structures using tree comparisons. {\itshape Computer applications in the biosciences\-: C\-A\-B\-I\-O\-S}, 6(4)\-:309--318, 1990.


\item[\label{_CITEREF_shapiro:1988}%
\mbox{[}12\mbox{]}]B.\-A. Shapiro. An algorithm for comparing multiple R\-N\-A secondary structures. {\itshape Computer applications in the biosciences\-: C\-A\-B\-I\-O\-S}, 4(3)\-:387--393, 1988.


\item[\label{_CITEREF_turner:2010}%
\mbox{[}13\mbox{]}]D.\-H. Turner and D.\-H. Mathews. N\-N\-D\-B\-: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. {\itshape Nucleic Acids Research}, 38(suppl 1)\-:D280--D282, 2010.


\item[\label{_CITEREF_zuker:1981}%
\mbox{[}14\mbox{]}]M.~Zuker and P.~Stiegler. Optimal computer folding of large R\-N\-A sequences using thermodynamics and auxiliary information. {\itshape Nucleic acids research}, 9(1)\-:133--148, 1981.


\end{DoxyDescription}