--- /dev/null
+\hypertarget{group__consensus__fold}{\section{Predicting Consensus Structures from Alignment(s)}
+\label{group__consensus__fold}\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+}
+
+
+compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments
+
+
+Collaboration diagram for Predicting Consensus Structures from Alignment(s)\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__consensus__fold}
+\end{center}
+\end{figure}
+\subsection*{Modules}
+\begin{DoxyCompactItemize}
+\item
+\hyperlink{group__consensus__mfe__fold}{M\-F\-E Consensus Structures for Sequence Alignment(s)}
+\item
+\hyperlink{group__consensus__pf__fold}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
+\item
+\hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
+\item
+\hyperlink{group__local__consensus__fold}{Local M\-F\-E consensus structures for Sequence Alignments}
+\end{DoxyCompactItemize}
+\subsection*{Files}
+\begin{DoxyCompactItemize}
+\item
+file \hyperlink{alifold_8h}{alifold.\-h}
+\begin{DoxyCompactList}\small\item\em compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item
+int \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\-\_\-mpi} (char $\ast$Alseq\mbox{[}$\,$\mbox{]}, int n\-\_\-seq, int length, int $\ast$mini)
+\begin{DoxyCompactList}\small\item\em Get the mean pairwise identity in steps from ?to?(ident) \end{DoxyCompactList}\item
+\hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}
+
+\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \end{DoxyCompactList}\item
+float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\-\_\-of\-\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\-\_\-seq, float $\ast$energy)
+\begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \end{DoxyCompactList}\item
+void \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\-\_\-ali\-\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
+\begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \end{DoxyCompactList}\item
+void \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays} (const char $\ast$$\ast$sequences, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
+\begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \end{DoxyCompactList}\item
+void \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays} (unsigned int n\-\_\-seq, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss)
+\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \end{DoxyCompactList}\item
+int \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\-\_\-alipf\-\_\-arrays} (short $\ast$$\ast$$\ast$S\-\_\-p, short $\ast$$\ast$$\ast$S5\-\_\-p, short $\ast$$\ast$$\ast$S3\-\_\-p, unsigned short $\ast$$\ast$$\ast$a2s\-\_\-p, char $\ast$$\ast$$\ast$Ss\-\_\-p, double $\ast$$\ast$qb\-\_\-p, double $\ast$$\ast$qm\-\_\-p, double $\ast$$\ast$q1k\-\_\-p, double $\ast$$\ast$qln\-\_\-p, short $\ast$$\ast$pscore)
+\begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \end{DoxyCompactList}\end{DoxyCompactItemize}
+\subsection*{Variables}
+\begin{DoxyCompactItemize}
+\item
+double \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\-\_\-fact}
+\begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \end{DoxyCompactList}\item
+double \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\-\_\-fact}
+\begin{DoxyCompactList}\small\item\em This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments Consensus structures can be predicted by a modified version of the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see\cite{hofacker:2002} and \cite{bernhart:2008}.
+
+\subsection{Function Documentation}
+\hypertarget{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-mpi@{get\-\_\-mpi}}
+\index{get\-\_\-mpi@{get\-\_\-mpi}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{get\-\_\-mpi}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-mpi (
+\begin{DoxyParamCaption}
+\item[{char $\ast$}]{Alseq\mbox{[}$\,$\mbox{]}, }
+\item[{int}]{n\-\_\-seq, }
+\item[{int}]{length, }
+\item[{int $\ast$}]{mini}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}
+
+
+Get the mean pairwise identity in steps from ?to?(ident)
+
+
+\begin{DoxyParams}{Parameters}
+{\em Alseq} & \\
+\hline
+{\em n\-\_\-seq} & The number of sequences in the alignment \\
+\hline
+{\em length} & The length of the alignment \\
+\hline
+{\em mini} & \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The mean pairwise identity
+\end{DoxyReturn}
+\hypertarget{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}}
+\index{energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{energy\-\_\-of\-\_\-alistruct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-alistruct (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{sequences, }
+\item[{const char $\ast$}]{structure, }
+\item[{int}]{n\-\_\-seq, }
+\item[{float $\ast$}]{energy}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}
+
+
+Calculate the free energy of a consensus structure given a set of aligned sequences.
+
+
+\begin{DoxyParams}{Parameters}
+{\em sequences} & The N\-U\-L\-L terminated array of sequences \\
+\hline
+{\em structure} & The consensus structure \\
+\hline
+{\em n\-\_\-seq} & The number of sequences in the alignment \\
+\hline
+{\em energy} & A pointer to an array of at least two floats that will hold the free energies (energy\mbox{[}0\mbox{]} will contain the free energy, energy\mbox{[}1\mbox{]} will be filled with the covariance energy term) \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+free energy in kcal/mol
+\end{DoxyReturn}
+\hypertarget{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}}
+\index{encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{encode\-\_\-ali\-\_\-sequence}]{\setlength{\rightskip}{0pt plus 5cm}void encode\-\_\-ali\-\_\-sequence (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$}]{sequence, }
+\item[{short $\ast$}]{S, }
+\item[{short $\ast$}]{s5, }
+\item[{short $\ast$}]{s3, }
+\item[{char $\ast$}]{ss, }
+\item[{unsigned short $\ast$}]{as, }
+\item[{int}]{circ}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}
+
+
+Get arrays with encoded sequence of the alignment.
+
+this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)
+
+
+\begin{DoxyParams}{Parameters}
+{\em sequence} & The gapped sequence from the alignment \\
+\hline
+{\em S} & pointer to an array that holds encoded sequence \\
+\hline
+{\em s5} & pointer to an array that holds the next base 5' of alignment position i \\
+\hline
+{\em s3} & pointer to an array that holds the next base 3' of alignment position i \\
+\hline
+{\em ss} & \\
+\hline
+{\em as} & \\
+\hline
+{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\
+\hline
+\end{DoxyParams}
+\hypertarget{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}}
+\index{alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{alloc\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void alloc\-\_\-sequence\-\_\-arrays (
+\begin{DoxyParamCaption}
+\item[{const char $\ast$$\ast$}]{sequences, }
+\item[{short $\ast$$\ast$$\ast$}]{S, }
+\item[{short $\ast$$\ast$$\ast$}]{S5, }
+\item[{short $\ast$$\ast$$\ast$}]{S3, }
+\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, }
+\item[{char $\ast$$\ast$$\ast$}]{Ss, }
+\item[{int}]{circ}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}
+
+
+Allocate memory for sequence array used to deal with aligned sequences.
+
+Note that these arrays will also be initialized according to the sequence alignment given
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em sequences} & The aligned sequences \\
+\hline
+{\em S} & A pointer to the array of encoded sequences \\
+\hline
+{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\
+\hline
+{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\
+\hline
+{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\
+\hline
+{\em Ss} & A pointer to the array that contains the ungapped sequence \\
+\hline
+{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\
+\hline
+\end{DoxyParams}
+\hypertarget{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}}
+\index{free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{free\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-sequence\-\_\-arrays (
+\begin{DoxyParamCaption}
+\item[{unsigned int}]{n\-\_\-seq, }
+\item[{short $\ast$$\ast$$\ast$}]{S, }
+\item[{short $\ast$$\ast$$\ast$}]{S5, }
+\item[{short $\ast$$\ast$$\ast$}]{S3, }
+\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, }
+\item[{char $\ast$$\ast$$\ast$}]{Ss}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}
+
+
+Free the memory of the sequence arrays used to deal with aligned sequences.
+
+This function frees the memory previously allocated with \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()}
+
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em n\-\_\-seq} & The number of aligned sequences \\
+\hline
+{\em S} & A pointer to the array of encoded sequences \\
+\hline
+{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\
+\hline
+{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\
+\hline
+{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\
+\hline
+{\em Ss} & A pointer to the array that contains the ungapped sequence \\
+\hline
+\end{DoxyParams}
+\hypertarget{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}}
+\index{get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{get\-\_\-alipf\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-alipf\-\_\-arrays (
+\begin{DoxyParamCaption}
+\item[{short $\ast$$\ast$$\ast$}]{S\-\_\-p, }
+\item[{short $\ast$$\ast$$\ast$}]{S5\-\_\-p, }
+\item[{short $\ast$$\ast$$\ast$}]{S3\-\_\-p, }
+\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s\-\_\-p, }
+\item[{char $\ast$$\ast$$\ast$}]{Ss\-\_\-p, }
+\item[{double $\ast$$\ast$}]{qb\-\_\-p, }
+\item[{double $\ast$$\ast$}]{qm\-\_\-p, }
+\item[{double $\ast$$\ast$}]{q1k\-\_\-p, }
+\item[{double $\ast$$\ast$}]{qln\-\_\-p, }
+\item[{short $\ast$$\ast$}]{pscore}
+\end{DoxyParamCaption}
+)}}\label{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}
+
+
+Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
+
+\begin{DoxyNote}{Note}
+To obtain meaningful pointers, call alipf\-\_\-fold first!
+\end{DoxyNote}
+\begin{DoxySeeAlso}{See Also}
+pf\-\_\-alifold(), \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold()}
+\end{DoxySeeAlso}
+
+\begin{DoxyParams}{Parameters}
+{\em S\-\_\-p} & A pointer to the 'S' array (integer representation of nucleotides) \\
+\hline
+{\em S5\-\_\-p} & A pointer to the 'S5' array \\
+\hline
+{\em S3\-\_\-p} & A pointer to the 'S3' array \\
+\hline
+{\em a2s\-\_\-p} & A pointer to the pair type matrix \\
+\hline
+{\em Ss\-\_\-p} & A pointer to the 'Ss' array \\
+\hline
+{\em qb\-\_\-p} & A pointer to the Q$^{\mbox{B}}$ matrix \\
+\hline
+{\em qm\-\_\-p} & A pointer to the Q$^{\mbox{M}}$ matrix \\
+\hline
+{\em q1k\-\_\-p} & A pointer to the 5' slice of the Q matrix ( $q1k(k) = Q(1, k)$) \\
+\hline
+{\em qln\-\_\-p} & A pointer to the 3' slice of the Q matrix ( $qln(l) = Q(l, n)$) \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+Non Zero if everything went fine, 0 otherwise
+\end{DoxyReturn}
+
+
+\subsection{Variable Documentation}
+\hypertarget{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!cv\-\_\-fact@{cv\-\_\-fact}}
+\index{cv\-\_\-fact@{cv\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{cv\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double cv\-\_\-fact}}\label{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}
+
+
+This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
+
+Default is 1. \hypertarget{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!nc\-\_\-fact@{nc\-\_\-fact}}
+\index{nc\-\_\-fact@{nc\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
+\subsubsection[{nc\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double nc\-\_\-fact}}\label{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}
+
+
+This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms.
+
+Default is 1.
\ No newline at end of file
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