https://github.com/cran/ape
Tip revision: 6f7033d8327bcce6c8a279fe7fffe84bfb1252ca authored by Emmanuel Paradis on 14 February 2017, 18:15:21 UTC
version 4.1
version 4.1
Tip revision: 6f7033d
nj.Rd
\name{nj}
\alias{nj}
\title{Neighbor-Joining Tree Estimation}
\description{
This function performs the neighbor-joining tree estimation of Saitou
and Nei (1987).
}
\usage{
nj(X)
}
\arguments{
\item{X}{a distance matrix; may be an object of class ``dist''.}
}
\value{
an object of class \code{"phylo"}.
}
\references{
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new
method for reconstructing phylogenetic trees. \emph{Molecular Biology
and Evolution}, \bold{4}, 406--425.
Studier, J. A. and Keppler, K. J. (1988) A note on the
neighbor-joining algorithm of Saitou and Nei. \emph{Molecular Biology
and Evolution}, \bold{5}, 729--731.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{write.tree}}, \code{\link{read.tree}},
\code{\link{dist.dna}}, \code{\link{bionj}},
\code{\link{fastme}}, \code{\link{njs}}
}
\examples{
### From Saitou and Nei (1987, Table 1):
x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
5, 6, 10, 9, 13, 8)
M <- matrix(0, 8, 8)
M[lower.tri(M)] <- x
M <- t(M)
M[lower.tri(M)] <- x
dimnames(M) <- list(1:8, 1:8)
tr <- nj(M)
plot(tr, "u")
### a less theoretical example
data(woodmouse)
trw <- nj(dist.dna(woodmouse))
plot(trw)
}
\keyword{models}