nj {ape} | R Documentation |
This function performs the neighbor-joining tree estimation of Saitou and Nei (1987).
nj(X)
X |
a distance matrix; may be an object of class ``dist''. |
The argument may be a square matrix (e.g. as estimated by
dist.dna
), a dist
object (estimated by
dist
).
an object of class "phylo"
.
Emmanuel Paradis paradis@isem.univ-montp2.fr
Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425.
write.tree
, read.tree
,
dist.dna
### 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(NA, 8, 8) M[row(M) > col(M)] <- x M[row(M) < col(M)] <- x diag(M) <- 0 rownames(M) <- colnames(M) <- 1:8 tr <- nj(M) plot(tr, "u") ### a less theoretical example data(woodmouse) trw <- nj(dist.dna(woodmouse)) plot(trw)