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 Studier, J. A. and Keppler, K. J. (1988) A note on the
23 neighbor-joining algorithm of Saitou and Nei. \emph{Molecular Biology
24 and Evolution}, \bold{5}, 729--731.
26 \author{Emmanuel Paradis}
28 \code{\link{write.tree}}, \code{\link{read.tree}},
29 \code{\link{dist.dna}}, \code{\link{bionj}},
33 ### From Saitou and Nei (1987, Table 1):
34 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
35 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
38 M[row(M) > col(M)] <- x
39 M[row(M) < col(M)] <- x
40 rownames(M) <- colnames(M) <- 1:8
43 ### a less theoretical example
45 trw <- nj(dist.dna(woodmouse))