R: Neighbor-Joining Tree Estimation

nj {ape} | R Documentation

## Neighbor-Joining Tree Estimation

### Description

This function performs the neighbor-joining tree estimation of Saitou and Nei (1987).

### Usage

    nj(X)

### Arguments

`X` | a distance matrix; may be an object of class “dist”.

### Value

an object of class `"phylo"`.

### Author(s)

Emmanuel Paradis

### References

Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406–425.

Studier, J. A. and Keppler, K. J. (1988) A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution, 5, 729–731.

### See Also

`write.tree`, `read.tree`, `dist.dna`, `bionj`, `fastme`, `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)

[Package ape version 4.1 Index]