1 \hypertarget{group__consensus__mfe__fold}{\section{M\-F\-E Consensus Structures for Sequence Alignment(s)}
2 \label{group__consensus__mfe__fold}\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
4 Collaboration diagram for M\-F\-E Consensus Structures for Sequence Alignment(s)\-:
9 \includegraphics[width=350pt]{group__consensus__mfe__fold}
12 \subsection*{Functions}
13 \begin{DoxyCompactItemize}
15 float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
16 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item
17 float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
18 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item
19 \hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}
21 \begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\end{DoxyCompactItemize}
24 \subsection{Detailed Description}
27 \subsection{Function Documentation}
28 \hypertarget{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!alifold@{alifold}}
29 \index{alifold@{alifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
30 \subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (
31 \begin{DoxyParamCaption}
32 \item[{const char $\ast$$\ast$}]{strings, }
33 \item[{char $\ast$}]{structure}
34 \end{DoxyParamCaption}
35 )}}\label{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}
38 Compute M\-F\-E and according consensus structure of an alignment of sequences.
40 This function predicts the consensus structure for the aligned 'sequences' and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.
42 Sufficient space must be allocated for 'structure' before calling \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()}.
45 \begin{DoxyParams}{Parameters}
46 {\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
48 {\em structure} & A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the M\-F\-E) \\
51 \begin{DoxyReturn}{Returns}
52 The free energy score in kcal/mol
54 \hypertarget{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{\index{M\-F\-E Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}!circalifold@{circalifold}}
55 \index{circalifold@{circalifold}!MFE Consensus Structures for Sequence Alignment(s)@{M\-F\-E Consensus Structures for Sequence Alignment(s)}}
56 \subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (
57 \begin{DoxyParamCaption}
58 \item[{const char $\ast$$\ast$}]{strings, }
59 \item[{char $\ast$}]{structure}
60 \end{DoxyParamCaption}
61 )}}\label{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}
64 Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear.
67 \begin{DoxyParams}{Parameters}
68 {\em strings} & A pointer to a N\-U\-L\-L terminated array of character arrays \\
70 {\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 M\-F\-E) \\
73 \begin{DoxyReturn}{Returns}
74 The free energy score in kcal/mol