\section{Modules}
Here is a list of all modules:\begin{DoxyCompactList}
\item \contentsline{section}{RNA Secondary Structure Folding}{\pageref{group__folding__routines}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Calculating Minimum Free Energy (MFE) Structures}{\pageref{group__mfe__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{MFE Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
\item \contentsline{section}{MFE Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
\item \contentsline{section}{Local MFE structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
\item \contentsline{section}{Calculating MFE representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Calculating Partition Functions and Pair Probabilities}{\pageref{group__pf__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Compute the structure with maximum expected accuracy (MEA)}{\pageref{group__mea__fold}}{}
\item \contentsline{section}{Compute the centroid structure}{\pageref{group__centroid__fold}}{}
\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Enumerating Suboptimal Structures}{\pageref{group__subopt__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Suboptimal structures according to Zuker et al. 1989}{\pageref{group__subopt__zuker}}{}
\item \contentsline{section}{Suboptimal structures within an energy band arround the MFE}{\pageref{group__subopt__wuchty}}{}
\item \contentsline{section}{Stochastic backtracking in the Ensemble}{\pageref{group__subopt__stochbt}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
\end{DoxyCompactList}
\end{DoxyCompactList}
\item \contentsline{section}{Calculate Secondary Structures of two RNAs upon Dimerization}{\pageref{group__cofold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{MFE Structures of two hybridized Sequences}{\pageref{group__mfe__cofold}}{}
\item \contentsline{section}{Partition Function for two hybridized Sequences}{\pageref{group__pf__cofold}}{}
\item \contentsline{section}{Partition Function for two hybridized Sequences as a stepwise Process}{\pageref{group__up__cofold}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Predicting Consensus Structures from Alignment(s)}{\pageref{group__consensus__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{MFE Consensus Structures for Sequence Alignment(s)}{\pageref{group__consensus__mfe__fold}}{}
\item \contentsline{section}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}{\pageref{group__consensus__pf__fold}}{}
\item \contentsline{section}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}{\pageref{group__consensus__stochbt}}{}
\item \contentsline{section}{Local MFE consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Predicting Locally stable structures of large sequences}{\pageref{group__local__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Local MFE structure Prediction and Z-\/scores}{\pageref{group__local__mfe__fold}}{}
\item \contentsline{section}{Partition functions for locally stable secondary structures}{\pageref{group__local__pf__fold}}{}
\item \contentsline{section}{Local MFE consensus structures for Sequence Alignments}{\pageref{group__local__consensus__fold}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Change and Precalculate Energy Parameter Sets and Boltzmann Factors}{\pageref{group__energy__parameters}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Reading/Writing energy parameter sets from/to File}{\pageref{group__energy__parameters__rw}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Converting energy parameter files}{\pageref{group__energy__parameters__convert}}{}
\end{DoxyCompactList}
\end{DoxyCompactList}
\item \contentsline{section}{Energy evaluation}{\pageref{group__eval}}{}
\item \contentsline{section}{Searching Sequences for Predefined Structures}{\pageref{group__inverse__fold}}{}
\item \contentsline{section}{Classified Dynamic Programming}{\pageref{group__class__fold}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Distance based partitioning of the Secondary Structure Space}{\pageref{group__kl__neighborhood}}{}
\begin{DoxyCompactList}
\item \contentsline{section}{Calculating MFE representatives of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__mfe}}{}
\item \contentsline{section}{Calculate Partition Functions of a Distance Based Partitioning}{\pageref{group__kl__neighborhood__pf}}{}
\item \contentsline{section}{Stochastic Backtracking of Structures from Distance Based Partitioning}{\pageref{group__kl__neighborhood__stochbt}}{}
\end{DoxyCompactList}
\item \contentsline{section}{Compute the Density of States}{\pageref{group__dos}}{}
\end{DoxyCompactList}
\end{DoxyCompactList}
\item \contentsline{section}{Parsing and Comparing -\/ Functions to Manipulate Structures}{\pageref{group__parse}}{}
\end{DoxyCompactList}
