3 \title{Neighbor-Joining Tree Estimation}
5 This function performs the neighbor-joining tree estimation of Saitou
12 \item{X}{a distance matrix; may be an object of class ``dist''.}
15 an object of class \code{"phylo"}.
18 Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new
19 method for reconstructing phylogenetic trees. \emph{Molecular Biology
20 and Evolution}, \bold{4}, 406--425.
22 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
24 \code{\link{write.tree}}, \code{\link{read.tree}},
25 \code{\link{dist.dna}}, \code{\link{mlphylo}}, \code{\link{bionj}},
29 ### From Saitou and Nei (1987, Table 1):
30 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
31 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
34 M[row(M) > col(M)] <- x
35 M[row(M) < col(M)] <- x
36 rownames(M) <- colnames(M) <- 1:8
39 ### a less theoretical example
41 trw <- nj(dist.dna(woodmouse))