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 \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{write.tree}}, \code{\link{read.tree}},
- \code{\link{dist.dna}}, \code{\link{mlphylo}}, \code{\link{bionj}},
- \code{\link{fastme}}
+ \code{\link{dist.dna}}, \code{\link{bionj}},
+ \code{\link{fastme}}, \code{\link{njs}}
}
\examples{
### From Saitou and Nei (1987, Table 1):
10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
5, 6, 10, 9, 13, 8)
M <- matrix(0, 8, 8)
-M[row(M) > col(M)] <- x
-M[row(M) < col(M)] <- x
-rownames(M) <- colnames(M) <- 1:8
+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