\HeaderA{needwunsQS}{(Deprecated) Needleman-Wunsch Global Alignment}{needwunsQS}
\aliasA{needwunsQS,character,character-method}{needwunsQS}{needwunsQS,character,character.Rdash.method}
\aliasA{needwunsQS,character,XString-method}{needwunsQS}{needwunsQS,character,XString.Rdash.method}
\aliasA{needwunsQS,XString,character-method}{needwunsQS}{needwunsQS,XString,character.Rdash.method}
\aliasA{needwunsQS,XString,XString-method}{needwunsQS}{needwunsQS,XString,XString.Rdash.method}
\aliasA{print.needwunsQS}{needwunsQS}{print.needwunsQS}
\keyword{models}{needwunsQS}
\keyword{methods}{needwunsQS}
\begin{Description}\relax
Simple gap implementation of Needleman-Wunsch global alignment algorithm.
\end{Description}
\begin{Usage}
\begin{verbatim}
needwunsQS(s1, s2, substmat, gappen = 8)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{s1, s2}] an R character vector of length 1 or an \LinkA{XString}{XString} object.
\item[\code{substmat}] matrix of alignment score values.
\item[\code{gappen}] penalty for introducing a gap in the alignment.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Follows specification of Durbin, Eddy, Krogh, Mitchison (1998).
This function has been deprecated and is being replaced by
\code{pairwiseAlignment}.
\end{Details}
\begin{Value}
An instance of class \code{"PairwiseAlignedXStringSet"}.
\end{Value}
\begin{Author}\relax
Vince Carey (\email{stvjc@channing.harvard.edu}) (original author) and H. Pages (current maintainer).
\end{Author}
\begin{References}\relax
R. Durbin, S. Eddy, A. Krogh, G. Mitchison,
Biological Sequence Analysis, Cambridge UP 1998, sec 2.3.
\end{References}
\begin{SeeAlso}\relax
\LinkA{pairwiseAlignment}{pairwiseAlignment},
\LinkA{PairwiseAlignedXStringSet-class}{PairwiseAlignedXStringSet.Rdash.class},
\LinkA{substitution.matrices}{substitution.matrices}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
  ## This function has been deprecated
  ## Use 'pairwiseAlignment' instead.

  ## nucleotide alignment
  mat <- matrix(-5L, nrow = 4, ncol = 4)
  for (i in seq_len(4)) mat[i, i] <- 0L
  rownames(mat) <- colnames(mat) <- DNA_ALPHABET[1:4]
  s1 <- DNAString(paste(sample(DNA_ALPHABET[1:4], 1000, replace=TRUE), collapse=""))
  s2 <- DNAString(paste(sample(DNA_ALPHABET[1:4], 1000, replace=TRUE), collapse=""))
  nw0 <- needwunsQS(s1, s2, mat, gappen = 0)
  nw1 <- needwunsQS(s1, s2, mat, gappen = 1)
  nw5 <- needwunsQS(s1, s2, mat, gappen = 5)

  ## amino acid alignment
  needwunsQS("PAWHEAE", "HEAGAWGHEE", substmat = "BLOSUM50")
## End(Not run)
\end{ExampleCode}
\end{Examples}

