\section{File List}
Here is a list of all documented files with brief descriptions:\begin{DoxyCompactList}
\item\contentsline{section}{{\bfseries mainpage.h} }{\pageref{mainpage_8h}}{}
\item\contentsline{section}{H/\hyperlink{2Dfold_8h}{2Dfold.h} (Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures )}{\pageref{2Dfold_8h}}{}
\item\contentsline{section}{H/\hyperlink{2Dpfold_8h}{2Dpfold.h} (Compute the partition function and stochastically sample secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures )}{\pageref{2Dpfold_8h}}{}
\item\contentsline{section}{H/{\bfseries ali\_\-plex.h} }{\pageref{ali__plex_8h}}{}
\item\contentsline{section}{H/\hyperlink{alifold_8h}{alifold.h} (Compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, )}{\pageref{alifold_8h}}{}
\item\contentsline{section}{H/{\bfseries aln\_\-util.h} }{\pageref{aln__util_8h}}{}
\item\contentsline{section}{H/\hyperlink{cofold_8h}{cofold.h} (MFE version of cofolding routines )}{\pageref{cofold_8h}}{}
\item\contentsline{section}{H/\hyperlink{convert__epars_8h}{convert\_\-epars.h} (Functions and definitions for energy parameter file format conversion )}{\pageref{convert__epars_8h}}{}
\item\contentsline{section}{H/\hyperlink{data__structures_8h}{data\_\-structures.h} (All datastructures and typedefs shared among the Vienna RNA Package can be found here )}{\pageref{data__structures_8h}}{}
\item\contentsline{section}{H/\hyperlink{dist__vars_8h}{dist\_\-vars.h} (Global variables for Distance-\/Package )}{\pageref{dist__vars_8h}}{}
\item\contentsline{section}{H/\hyperlink{duplex_8h}{duplex.h} (Duplex folding function declarations )}{\pageref{duplex_8h}}{}
\item\contentsline{section}{H/\hyperlink{edit__cost_8h}{edit\_\-cost.h} (Global variables for Edit Costs included by treedist.c and stringdist.c )}{\pageref{edit__cost_8h}}{}
\item\contentsline{section}{H/\hyperlink{energy__const_8h}{energy\_\-const.h} (Energy constants )}{\pageref{energy__const_8h}}{}
\item\contentsline{section}{H/{\bfseries energy\_\-par.h} }{\pageref{energy__par_8h}}{}
\item\contentsline{section}{H/\hyperlink{findpath_8h}{findpath.h} (Compute direct refolding paths between two secondary structures )}{\pageref{findpath_8h}}{}
\item\contentsline{section}{H/\hyperlink{fold_8h}{fold.h} (MFE calculations and energy evaluations for single RNA sequences )}{\pageref{fold_8h}}{}
\item\contentsline{section}{H/\hyperlink{fold__vars_8h}{fold\_\-vars.h} (Here all all declarations of the global variables used throughout RNAlib )}{\pageref{fold__vars_8h}}{}
\item\contentsline{section}{H/\hyperlink{inverse_8h}{inverse.h} (Inverse folding routines )}{\pageref{inverse_8h}}{}
\item\contentsline{section}{H/\hyperlink{Lfold_8h}{Lfold.h} (Predicting local MFE structures of large sequences )}{\pageref{Lfold_8h}}{}
\item\contentsline{section}{H/\hyperlink{loop__energies_8h}{loop\_\-energies.h} (Energy evaluation for MFE and partition function calculations )}{\pageref{loop__energies_8h}}{}
\item\contentsline{section}{H/\hyperlink{LPfold_8h}{LPfold.h} (Function declarations of partition function variants of the Lfold algorithm )}{\pageref{LPfold_8h}}{}
\item\contentsline{section}{H/\hyperlink{MEA_8h}{MEA.h} (Computes a MEA (maximum expected accuracy) structure )}{\pageref{MEA_8h}}{}
\item\contentsline{section}{H/\hyperlink{mm_8h}{mm.h} (Several Maximum Matching implementations )}{\pageref{mm_8h}}{}
\item\contentsline{section}{H/\hyperlink{naview_8h}{naview.h} }{\pageref{naview_8h}}{}
\item\contentsline{section}{H/{\bfseries pair\_\-mat.h} }{\pageref{pair__mat_8h}}{}
\item\contentsline{section}{H/\hyperlink{params_8h}{params.h} (Several functions to obtain (pre)scaled energy parameter data containers )}{\pageref{params_8h}}{}
\item\contentsline{section}{H/\hyperlink{part__func_8h}{part\_\-func.h} (Partition function of single RNA sequences )}{\pageref{part__func_8h}}{}
\item\contentsline{section}{H/\hyperlink{part__func__co_8h}{part\_\-func\_\-co.h} (Partition function for two RNA sequences )}{\pageref{part__func__co_8h}}{}
\item\contentsline{section}{H/\hyperlink{part__func__up_8h}{part\_\-func\_\-up.h} (Partition Function Cofolding as stepwise process )}{\pageref{part__func__up_8h}}{}
\item\contentsline{section}{H/{\bfseries PKplex.h} }{\pageref{PKplex_8h}}{}
\item\contentsline{section}{H/{\bfseries plex.h} }{\pageref{plex_8h}}{}
\item\contentsline{section}{H/\hyperlink{plot__layouts_8h}{plot\_\-layouts.h} (Secondary structure plot layout algorithms )}{\pageref{plot__layouts_8h}}{}
\item\contentsline{section}{H/{\bfseries ProfileAln.h} }{\pageref{ProfileAln_8h}}{}
\item\contentsline{section}{H/\hyperlink{profiledist_8h}{profiledist.h} }{\pageref{profiledist_8h}}{}
\item\contentsline{section}{H/\hyperlink{PS__dot_8h}{PS\_\-dot.h} (Various functions for plotting RNA secondary structures, dot-\/plots and other visualizations )}{\pageref{PS__dot_8h}}{}
\item\contentsline{section}{H/\hyperlink{read__epars_8h}{read\_\-epars.h} (Functions to read and write energy parameter sets from/to files )}{\pageref{read__epars_8h}}{}
\item\contentsline{section}{H/{\bfseries ribo.h} }{\pageref{ribo_8h}}{}
\item\contentsline{section}{H/\hyperlink{RNAstruct_8h}{RNAstruct.h} (Parsing and Coarse Graining of Structures )}{\pageref{RNAstruct_8h}}{}
\item\contentsline{section}{H/{\bfseries snofold.h} }{\pageref{snofold_8h}}{}
\item\contentsline{section}{H/{\bfseries snoop.h} }{\pageref{snoop_8h}}{}
\item\contentsline{section}{H/\hyperlink{stringdist_8h}{stringdist.h} (Functions for String Alignment )}{\pageref{stringdist_8h}}{}
\item\contentsline{section}{H/\hyperlink{subopt_8h}{subopt.h} (RNAsubopt and density of states declarations )}{\pageref{subopt_8h}}{}
\item\contentsline{section}{H/{\bfseries svm\_\-utils.h} }{\pageref{svm__utils_8h}}{}
\item\contentsline{section}{H/\hyperlink{treedist_8h}{treedist.h} (Functions for \hyperlink{structTree}{Tree} Edit Distances )}{\pageref{treedist_8h}}{}
\item\contentsline{section}{H/\hyperlink{utils_8h}{utils.h} (Various utility-\/ and helper-\/functions used throughout the Vienna RNA package )}{\pageref{utils_8h}}{}
\item\contentsline{section}{lib/\hyperlink{1_88_84__epars_8h}{1.8.4\_\-epars.h} (Free energy parameters for parameter file conversion )}{\pageref{1_88_84__epars_8h}}{}
\item\contentsline{section}{lib/\hyperlink{1_88_84__intloops_8h}{1.8.4\_\-intloops.h} (Free energy parameters for interior loop contributions needed by the parameter file conversion functions )}{\pageref{1_88_84__intloops_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl11.h} }{\pageref{intl11_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl11dH.h} }{\pageref{intl11dH_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl21.h} }{\pageref{intl21_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl21dH.h} }{\pageref{intl21dH_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl22.h} }{\pageref{intl22_8h}}{}
\item\contentsline{section}{lib/{\bfseries intl22dH.h} }{\pageref{intl22dH_8h}}{}
\item\contentsline{section}{lib/{\bfseries list.h} }{\pageref{list_8h}}{}
\end{DoxyCompactList}
