\hypertarget{group__consensus__mfe__fold}{
\section{MFE Consensus Structures for Sequence Alignment(s)}
\label{group__consensus__mfe__fold}\index{MFE Consensus Structures for Sequence Alignment(s)@{MFE Consensus Structures for Sequence Alignment(s)}}
}


Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=292pt]{group__consensus__mfe__fold}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute MFE and according consensus structure of an alignment of sequences. \item\end{DoxyCompactList}\item 
float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \item\end{DoxyCompactList}\item 
\hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{
void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\_\-alifold\_\-arrays} (void)}
\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}

\begin{DoxyCompactList}\small\item\em Free the memory occupied by MFE alifold functions. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Function Documentation}
\hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{
\index{consensus\_\-mfe\_\-fold@{consensus\_\-mfe\_\-fold}!alifold@{alifold}}
\index{alifold@{alifold}!consensus_mfe_fold@{consensus\_\-mfe\_\-fold}}
\subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (const char $\ast$$\ast$ {\em strings}, \/  char $\ast$ {\em structure})}}
\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}


Compute MFE and according consensus structure of an alignment of sequences. This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.

Sufficient space must be allocated for 'structure' before calling \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()}.


\begin{DoxyParams}{Parameters}
\item[{\em strings}]A pointer to a NULL terminated array of character arrays \item[{\em structure}]A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy score in kcal/mol 
\end{DoxyReturn}
\hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{
\index{consensus\_\-mfe\_\-fold@{consensus\_\-mfe\_\-fold}!circalifold@{circalifold}}
\index{circalifold@{circalifold}!consensus_mfe_fold@{consensus\_\-mfe\_\-fold}}
\subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (const char $\ast$$\ast$ {\em strings}, \/  char $\ast$ {\em structure})}}
\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}


Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. 
\begin{DoxyParams}{Parameters}
\item[{\em strings}]A pointer to a NULL terminated array of character arrays \item[{\em structure}]A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
The free energy score in kcal/mol 
\end{DoxyReturn}
