https://github.com/cran/ape
Tip revision: 896233843123720089ba02c12a01772044a04979 authored by Emmanuel Paradis on 29 March 2010, 00:00:00 UTC
version 2.5-1
version 2.5-1
Tip revision: 8962338
write.nexus.Rd
\name{write.nexus}
\alias{write.nexus}
\title{Write Tree File in Nexus Format}
\usage{
write.nexus(..., file = "", translate = TRUE, original.data = TRUE)
}
\arguments{
\item{\dots}{either (i) a single object of class \code{"phylo"}, (ii) a
series of such objects separated by commas, or (iii) a list
containing such objects.}
\item{file}{a file name specified by either a variable of mode character,
or a double-quoted string; if \code{file = ""} (the default) then the
tree is written on the standard output connection.}
\item{translate}{a logical, if \code{TRUE} (the default) a translation
of the tip labels is done which are replaced in the parenthetic
representation with tokens.}
\item{original.data}{a logical, if \code{TRUE} (the default) the
data in the original NEXUS file are eventually written in
\code{"file"} (see below).}
}
\description{
This function writes trees in a file with the NEXUS format.
}
\details{
If \code{original.data = TRUE}, the file as specified by the attribute
\code{"origin"} of the first tree is read and its data (except the
trees) are written in \code{file}.
If several trees are given, they must have all the same tip labels.
If among the objects given some are not trees of class \code{"phylo"},
they are simply skipped and not written to the file.
}
\value{
None (invisible `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{Emmanuel Paradis}
\seealso{
\code{\link{read.nexus}}, \code{\link{read.tree}},
\code{\link{write.tree}}, \code{\link{read.nexus.data}},
\code{\link{write.nexus.data}}
}
\keyword{manip}
\keyword{IO}