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\name{write.phyloXML}
\alias{write.phyloXML}
\title{Write Tree File in phyloXML Format}
\usage{
write.phyloXML(phy, file = "", tree.names = FALSE)
}
\arguments{
\item{phy}{an object of class \code{"phylo"} or \code{"multiPhylo"}.}
\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 (i.e. the console).}
\item{tree.names}{either a logical or a vector of mode character
specifying whether or which tree names should be written to the file.}
}
\description{
This function writes trees to a file of phyloXML format.
}
\details{
If several trees are given, they will be represented as multiple
<phylogeny> elements. Contrary to \code{\link{write.nexus}}, the trees
need not have the same tip labels.
When \code{tree.names} is \code{TRUE}, the tree names will be always
added as <name> tags to each phylogeny element. If the \code{phy}
object is unnamed, then the names will be automatically generated
from the tree indices as "tree<index>" (e.g. tree1, tree2, ...). If
\code{tree.names} is a character vector, the specified names will be
used instead.
Branch lengths, labels, and rootedness are preserved in the phyloXML
file.
}
\value{
None (invisible \code{NULL}).
}
\references{
Han, M. V. and Zmasek, C. M. (2009) phyloXML: XML for evolutionary biology and
comparative genomics. \emph{BMC Bioinformatics}, \bold{10}, 356.
}
\author{Federico Marotta}
\seealso{
\code{\link{read.tree}}, \code{\link{write.tree}},
\code{\link{read.nexus}}, \code{\link{write.nexus}},
\code{\link{read.nexus.data}}, \code{\link{write.nexus.data}}
}
\keyword{manip}
\keyword{IO}
|
