\usage{
read.dna(file, format = "interleaved", skip = 0,
nlines = 0, comment.char = "#", seq.names = NULL,
- as.character = FALSE)
+ as.character = FALSE, as.matrix = NULL)
}
\arguments{
\item{file}{a file name specified by either a variable of mode character,
names read in the file are used.}
\item{as.character}{a logical controlling whether to return the
sequences as an object of class \code{"DNAbin"} (the default).}
+ \item{as.matrix}{(used if \code{format = "fasta"}) one of the three
+ followings: (i) \code{NULL}: returns the sequences in a matrix if
+ they are of the same length, otherwise in a list; (ii) \code{TRUE}:
+ returns the sequences in a matrix, or stops with an error if they
+ are of different lengths; (iii) \code{FALSE}: always returns the
+ sequences in a list.}
}
\description{
This function reads DNA sequences in a file, and returns a matrix or a
sequential formats, see below). The names of the sequences are read in
the file unless the `seq.names' option is used. Particularities for
each format are detailed below.
-
+
\itemize{
\item{Interleaved:}{the function starts to read the sequences when it
finds 10 contiguous characters belonging to the ambiguity code of
\code{\link{read.GenBank}}, \code{\link{write.dna}},
\code{\link{DNAbin}}, \code{\link{dist.dna}}, \code{\link{woodmouse}}
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\examples{
### a small extract from `data(woddmouse)'
cat("3 40",