\name{write.nexus.data}
\alias{write.nexus.data}
\title{Write Character Data in NEXUS Format}
\description{
  This function writes in a file a list of data in the NEXUS format. The
  names of the vectors of the list are used as taxon names.

  For the moment, only sequence data (DNA or protein) are supported.
}
\usage{
write.nexus.data(x, file, format = "dna", datablock = TRUE,
                 interleaved = TRUE, charsperline = NULL,
                 gap = NULL, missing = NULL)
}
\arguments{
  \item{x}{a matrix or a list of data each made of a single vector
    of mode character where each element is a character state (e.g.,
    \dQuote{A}, \dQuote{C}, \dots) Objects of class of \dQuote{DNAbin}
    are accepted.}
  \item{file}{a file name specified by either a variable of mode
    character, or a double-quoted string.}
  \item{format}{a character string specifying the format of the
    sequences. Four choices are possible: \code{"dna"} (the default)
    \code{"protein"}, \code{"standard"} or \code{"continuous"} or any
    unambiguous abbreviation of these (case insensitive).}
  \item{datablock}{a logical, if \code{TRUE} the data are written in a
    single DATA block. If \code{FALSE}, the data are written in TAXA and
    CHARACTER blocks. Default is \code{TRUE}.}
  \item{interleaved}{a logical, if \code{TRUE} the data is written in
    interleaved format with number of characters per line as specified
    with \code{charsperline = numerical_value}. If \code{FALSE}, the
    data are written in sequential format. Default is \code{TRUE}.}
  \item{charsperline}{a numeric value specifying the number of
    characters per line when used with \code{interleaved =
      TRUE}. Default is 80.}
  \item{gap}{a character specifying the symbol for gap. Default is
    \dQuote{\code{-}}.}
  \item{missing}{a character specifying the symbol for missing
    data. Default is \dQuote{\code{?}}.}
}
\details{
  If the sequences have no names, then they are given \dQuote{1},
  \dQuote{2}, ..., as names in the file.

  Sequences must be all of the same length.
}
\value{
  None (invisible \sQuote{NULL}).
}
\references{
  Maddison, D. R., Swofford, D. L. and Maddison, W. P. (1997) NEXUS: an
  extensible file format for systematic information. \emph{Systematic
    Biology}, \bold{46}, 590--621.
}
\author{Johan Nylander \email{nylander@scs.fsu.edu} and Thomas Guillerme}
\seealso{
  \code{\link{read.nexus}},\code{\link{write.nexus}},
  \code{\link{read.nexus.data}}
}
\examples{
\dontrun{
## Write interleaved DNA data with 100 characters per line in a DATA block
data(woodmouse)
write.nexus.data(woodmouse, file= "wood.ex.nex", interleaved = TRUE, charsperline = 100)
## Write sequential DNA data in TAXA and CHARACTERS blocks
data(cynipids)
write.nexus.data(cynipids, file = "cyn.ex.nex", format = "protein",
                 datablock = FALSE, interleaved = FALSE)
unlink(c("wood.ex.nex", "cyn.ex.nex"))
}}
\keyword{file}