# nj

From ape v2.1-1
by Emmanuel Paradis

##### Neighbor-Joining Tree Estimation

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

- Keywords
- models

##### Usage

`nj(X)`

##### Arguments

- X
- a distance matrix; may be an object of class ``dist''.

##### Value

- an object of class
`"phylo"`

.

##### 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.

##### See Also

##### 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[row(M) > col(M)] <- x
M[row(M) < col(M)] <- x
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)
```

*Documentation reproduced from package ape, version 2.1-1, License: GPL (>= 2)*

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