NJ: Neighbor-Joining

In phangorn: Phylogenetic Reconstruction and Analysis

Neighbor-Joining

Description

This function performs the neighbor-joining tree estimation of Saitou and Nei (1987). UNJ is the unweighted version from Gascuel (1997).

Usage

NJ(x)

UNJ(x)

Arguments

x	A distance matrix.

Value

an object of class "phylo".

Author(s)

Klaus P. Schliep [e-mail]

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, 6, 729–731.

Gascuel, O. (1997) Concerning the NJ algorithm and its unweighted version, UNJ. in Birkin et. al. Mathematical Hierarchies and Biology, 149–170.

See Also

nj, dist.dna, dist.hamming, upgma, fastme

Examples

data(Laurasiatherian)
dm <- dist.ml(Laurasiatherian)
tree <- NJ(dm)
plot(tree)

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.