\hypertarget{alifold_8h}{
\section{H/alifold.h File Reference}
\label{alifold_8h}\index{H/alifold.h@{H/alifold.h}}
}


compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, .  
Include dependency graph for alifold.h:\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
void \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\_\-alifold\_\-params} (void)
\begin{DoxyCompactList}\small\item\em Update the energy parameters for alifold function. \item\end{DoxyCompactList}\item 
float \hyperlink{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute MFE and according consensus structure of an alignment of sequences. \item\end{DoxyCompactList}\item 
float \hyperlink{alifold_8h_adbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\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{alifold_8h_a72095e4554b5d577250ea14c42acc49e}{
void \hyperlink{alifold_8h_a72095e4554b5d577250ea14c42acc49e}{free\_\-alifold\_\-arrays} (void)}
\label{alifold_8h_a72095e4554b5d577250ea14c42acc49e}

\begin{DoxyCompactList}\small\item\em Free the memory occupied by MFE alifold functions. \item\end{DoxyCompactList}\item 
int \hyperlink{alifold_8h_aa2d600be90844094ec145ea14a314d2f}{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). \item\end{DoxyCompactList}\item 
\hypertarget{alifold_8h_a5e125c9586fcd4e2e1559fe76f7289cc}{
float $\ast$$\ast$ \hyperlink{alifold_8h_a5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}
\label{alifold_8h_a5e125c9586fcd4e2e1559fe76f7289cc}

\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \item\end{DoxyCompactList}\item 
float \hyperlink{alifold_8h_a1c48869c03b49a342bf4cbdd61900081}{energy\_\-of\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\_\-seq, float $\ast$energy)
\begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \item\end{DoxyCompactList}\item 
void \hyperlink{alifold_8h_aa3e40277c837d6f7603afe319884c786}{encode\_\-ali\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
\begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \item\end{DoxyCompactList}\item 
void \hyperlink{alifold_8h_a8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays} (const char $\ast$$\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. \item\end{DoxyCompactList}\item 
void \hyperlink{alifold_8h_a298a420a8c879202e2617b3f724fde38}{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. \item\end{DoxyCompactList}\item 
float \hyperlink{alifold_8h_a4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\_\-fold\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\_\-paramT} $\ast$parameters, int calculate\_\-bppm, int is\_\-constrained, int is\_\-circular)
\item 
float \hyperlink{alifold_8h_ad32ded7d753ccaf211ab35782d1f42a9}{alipf\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{part__func_8h_adc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. \item\end{DoxyCompactList}\item 
float \hyperlink{alifold_8h_a6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\item 
FLT\_\-OR\_\-DBL $\ast$ \hyperlink{alifold_8h_a11b6ab8bd9be1821fea352b190a01cab}{export\_\-ali\_\-bppm} (void)
\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \item\end{DoxyCompactList}\item 
char $\ast$ \hyperlink{alifold_8h_a0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack} (double $\ast$prob)
\begin{DoxyCompactList}\small\item\em Sample a consensus secondary structure from the Boltzmann ensemble according its probability\par
. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
double \hyperlink{alifold_8h_af3cbac6ff5d706d6e414677841ddf94c}{cv\_\-fact}
\begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \item\end{DoxyCompactList}\item 
double \hyperlink{alifold_8h_a502948a122a2af5b914355b1f3ea2f61}{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. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, . ..) for RNA sequence alignments 

\subsection{Function Documentation}
\hypertarget{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{
\index{alifold.h@{alifold.h}!update\_\-alifold\_\-params@{update\_\-alifold\_\-params}}
\index{update\_\-alifold\_\-params@{update\_\-alifold\_\-params}!alifold.h@{alifold.h}}
\subsubsection[{update\_\-alifold\_\-params}]{\setlength{\rightskip}{0pt plus 5cm}void update\_\-alifold\_\-params (void)}}
\label{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}


Update the energy parameters for alifold function. Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} \hypertarget{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}{
\index{alifold.h@{alifold.h}!alifold@{alifold}}
\index{alifold@{alifold}!alifold.h@{alifold.h}}
\subsubsection[{alifold}]{\setlength{\rightskip}{0pt plus 5cm}float alifold (const char $\ast$$\ast$ {\em strings}, \/  char $\ast$ {\em structure})}}
\label{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}


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{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}{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{alifold_8h_adbd3b0b1c144cbfb4efe704b2b260f96}{
\index{alifold.h@{alifold.h}!circalifold@{circalifold}}
\index{circalifold@{circalifold}!alifold.h@{alifold.h}}
\subsubsection[{circalifold}]{\setlength{\rightskip}{0pt plus 5cm}float circalifold (const char $\ast$$\ast$ {\em strings}, \/  char $\ast$ {\em structure})}}
\label{alifold_8h_adbd3b0b1c144cbfb4efe704b2b260f96}


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}
\hypertarget{alifold_8h_aa2d600be90844094ec145ea14a314d2f}{
\index{alifold.h@{alifold.h}!get\_\-mpi@{get\_\-mpi}}
\index{get\_\-mpi@{get\_\-mpi}!alifold.h@{alifold.h}}
\subsubsection[{get\_\-mpi}]{\setlength{\rightskip}{0pt plus 5cm}int get\_\-mpi (char $\ast$ {\em Alseq}\mbox{[}$\,$\mbox{]}, \/  int {\em n\_\-seq}, \/  int {\em length}, \/  int $\ast$ {\em mini})}}
\label{alifold_8h_aa2d600be90844094ec145ea14a314d2f}


Get the mean pairwise identity in steps from ?to?(ident). 
\begin{DoxyParams}{Parameters}
\item[{\em Alseq}]\item[{\em n\_\-seq}]The number of sequences in the alignment \item[{\em length}]The length of the alignment \item[{\em mini}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}
The mean pairwise identity 
\end{DoxyReturn}
\hypertarget{alifold_8h_a1c48869c03b49a342bf4cbdd61900081}{
\index{alifold.h@{alifold.h}!energy\_\-of\_\-alistruct@{energy\_\-of\_\-alistruct}}
\index{energy\_\-of\_\-alistruct@{energy\_\-of\_\-alistruct}!alifold.h@{alifold.h}}
\subsubsection[{energy\_\-of\_\-alistruct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-alistruct (const char $\ast$$\ast$ {\em sequences}, \/  const char $\ast$ {\em structure}, \/  int {\em n\_\-seq}, \/  float $\ast$ {\em energy})}}
\label{alifold_8h_a1c48869c03b49a342bf4cbdd61900081}


Calculate the free energy of a consensus structure given a set of aligned sequences. 
\begin{DoxyParams}{Parameters}
\item[{\em sequences}]The NULL terminated array of sequences \item[{\em structure}]The consensus structure \item[{\em n\_\-seq}]The number of sequences in the alignment \item[{\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) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
free energy in kcal/mol 
\end{DoxyReturn}
\hypertarget{alifold_8h_aa3e40277c837d6f7603afe319884c786}{
\index{alifold.h@{alifold.h}!encode\_\-ali\_\-sequence@{encode\_\-ali\_\-sequence}}
\index{encode\_\-ali\_\-sequence@{encode\_\-ali\_\-sequence}!alifold.h@{alifold.h}}
\subsubsection[{encode\_\-ali\_\-sequence}]{\setlength{\rightskip}{0pt plus 5cm}void encode\_\-ali\_\-sequence (const char $\ast$ {\em sequence}, \/  short $\ast$ {\em S}, \/  short $\ast$ {\em s5}, \/  short $\ast$ {\em s3}, \/  char $\ast$ {\em ss}, \/  unsigned short $\ast$ {\em as}, \/  int {\em circ})}}
\label{alifold_8h_aa3e40277c837d6f7603afe319884c786}


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}
\item[{\em sequence}]The gapped sequence from the alignment \item[{\em S}]pointer to an array that holds encoded sequence \item[{\em s5}]pointer to an array that holds the next base 5' of alignment position i \item[{\em s3}]pointer to an array that holds the next base 3' of alignment position i \item[{\em ss}]\item[{\em as}]\item[{\em circ}]assume the molecules to be circular instead of linear (circ=0) \end{DoxyParams}
\hypertarget{alifold_8h_a8a560930f7f2582cc3967723a86cfdfa}{
\index{alifold.h@{alifold.h}!alloc\_\-sequence\_\-arrays@{alloc\_\-sequence\_\-arrays}}
\index{alloc\_\-sequence\_\-arrays@{alloc\_\-sequence\_\-arrays}!alifold.h@{alifold.h}}
\subsubsection[{alloc\_\-sequence\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void alloc\_\-sequence\_\-arrays (const char $\ast$$\ast$ {\em sequences}, \/  short $\ast$$\ast$$\ast$ {\em S}, \/  short $\ast$$\ast$$\ast$ {\em S5}, \/  short $\ast$$\ast$$\ast$ {\em S3}, \/  unsigned short $\ast$$\ast$$\ast$ {\em a2s}, \/  char $\ast$$\ast$$\ast$ {\em Ss}, \/  int {\em circ})}}
\label{alifold_8h_a8a560930f7f2582cc3967723a86cfdfa}


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{alifold_8h_a298a420a8c879202e2617b3f724fde38}{free\_\-sequence\_\-arrays()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em sequences}]The aligned sequences \item[{\em S}]A pointer to the array of encoded sequences \item[{\em S5}]A pointer to the array that contains the next 5' nucleotide of a sequence position \item[{\em S3}]A pointer to the array that contains the next 3' nucleotide of a sequence position \item[{\em a2s}]A pointer to the array that contains the alignment to sequence position mapping \item[{\em Ss}]A pointer to the array that contains the ungapped sequence \item[{\em circ}]assume the molecules to be circular instead of linear (circ=0) \end{DoxyParams}
\hypertarget{alifold_8h_a298a420a8c879202e2617b3f724fde38}{
\index{alifold.h@{alifold.h}!free\_\-sequence\_\-arrays@{free\_\-sequence\_\-arrays}}
\index{free\_\-sequence\_\-arrays@{free\_\-sequence\_\-arrays}!alifold.h@{alifold.h}}
\subsubsection[{free\_\-sequence\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void free\_\-sequence\_\-arrays (unsigned int {\em n\_\-seq}, \/  short $\ast$$\ast$$\ast$ {\em S}, \/  short $\ast$$\ast$$\ast$ {\em S5}, \/  short $\ast$$\ast$$\ast$ {\em S3}, \/  unsigned short $\ast$$\ast$$\ast$ {\em a2s}, \/  char $\ast$$\ast$$\ast$ {\em Ss})}}
\label{alifold_8h_a298a420a8c879202e2617b3f724fde38}


Free the memory of the sequence arrays used to deal with aligned sequences. This function frees the memory previously allocated with \hyperlink{alifold_8h_a8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays()}

\begin{DoxySeeAlso}{See also}
\hyperlink{alifold_8h_a8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays()}
\end{DoxySeeAlso}

\begin{DoxyParams}{Parameters}
\item[{\em n\_\-seq}]The number of aligned sequences \item[{\em S}]A pointer to the array of encoded sequences \item[{\em S5}]A pointer to the array that contains the next 5' nucleotide of a sequence position \item[{\em S3}]A pointer to the array that contains the next 3' nucleotide of a sequence position \item[{\em a2s}]A pointer to the array that contains the alignment to sequence position mapping \item[{\em Ss}]A pointer to the array that contains the ungapped sequence \end{DoxyParams}
\hypertarget{alifold_8h_a4d2ff54d8210fc7cceeeff389d4dbd1d}{
\index{alifold.h@{alifold.h}!alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}}
\index{alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}!alifold.h@{alifold.h}}
\subsubsection[{alipf\_\-fold\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold\_\-par (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl}, \/  {\bf pf\_\-paramT} $\ast$ {\em parameters}, \/  int {\em calculate\_\-bppm}, \/  int {\em is\_\-constrained}, \/  int {\em is\_\-circular})}}
\label{alifold_8h_a4d2ff54d8210fc7cceeeff389d4dbd1d}

\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\item[{\em parameters}]\item[{\em calculate\_\-bppm}]\item[{\em is\_\-constrained}]\item[{\em is\_\-circular}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{alifold_8h_ad32ded7d753ccaf211ab35782d1f42a9}{
\index{alifold.h@{alifold.h}!alipf\_\-fold@{alipf\_\-fold}}
\index{alipf\_\-fold@{alipf\_\-fold}!alifold.h@{alifold.h}}
\subsubsection[{alipf\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
\label{alifold_8h_ad32ded7d753ccaf211ab35782d1f42a9}


The partition function version of \hyperlink{alifold_8h_a4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{part__func_8h_adc3db3d98742427e7001a7fd36ef28c2}{pf\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\_\-info} structs. The list is terminated by the first entry with pi.i = 0.


\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{alifold_8h_a6b4dde1d43b79ab3753508c46cf50363}{
\index{alifold.h@{alifold.h}!alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}}
\index{alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}!alifold.h@{alifold.h}}
\subsubsection[{alipf\_\-circ\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-circ\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
\label{alifold_8h_a6b4dde1d43b79ab3753508c46cf50363}

\begin{DoxyParams}{Parameters}
\item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}

\end{DoxyReturn}
\hypertarget{alifold_8h_a11b6ab8bd9be1821fea352b190a01cab}{
\index{alifold.h@{alifold.h}!export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}}
\index{export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}!alifold.h@{alifold.h}}
\subsubsection[{export\_\-ali\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}FLT\_\-OR\_\-DBL$\ast$ export\_\-ali\_\-bppm (void)}}
\label{alifold_8h_a11b6ab8bd9be1821fea352b190a01cab}


Get a pointer to the base pair probability array. Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}


\begin{DoxySeeAlso}{See also}
\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_\-iindx()} 
\end{DoxySeeAlso}
\begin{DoxyReturn}{Returns}
A pointer to the base pair probability array 
\end{DoxyReturn}
\hypertarget{alifold_8h_a0df40248788f0fb17ebdc59d74116d1c}{
\index{alifold.h@{alifold.h}!alipbacktrack@{alipbacktrack}}
\index{alipbacktrack@{alipbacktrack}!alifold.h@{alifold.h}}
\subsubsection[{alipbacktrack}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ alipbacktrack (double $\ast$ {\em prob})}}
\label{alifold_8h_a0df40248788f0fb17ebdc59d74116d1c}


Sample a consensus secondary structure from the Boltzmann ensemble according its probability\par
. 
\begin{DoxyParams}{Parameters}
\item[{\em prob}]to be described (berni) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
A sampled consensus secondary structure in dot-\/bracket notation 
\end{DoxyReturn}


\subsection{Variable Documentation}
\hypertarget{alifold_8h_af3cbac6ff5d706d6e414677841ddf94c}{
\index{alifold.h@{alifold.h}!cv\_\-fact@{cv\_\-fact}}
\index{cv\_\-fact@{cv\_\-fact}!alifold.h@{alifold.h}}
\subsubsection[{cv\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double {\bf cv\_\-fact}}}
\label{alifold_8h_af3cbac6ff5d706d6e414677841ddf94c}


This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. Default is 1. \hypertarget{alifold_8h_a502948a122a2af5b914355b1f3ea2f61}{
\index{alifold.h@{alifold.h}!nc\_\-fact@{nc\_\-fact}}
\index{nc\_\-fact@{nc\_\-fact}!alifold.h@{alifold.h}}
\subsubsection[{nc\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double {\bf nc\_\-fact}}}
\label{alifold_8h_a502948a122a2af5b914355b1f3ea2f61}


This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. Default is 1. 