Neighbor-Joining

This function performs the neighbor-joining tree estimation of Saitou and Nei (1987); Studier and Keppler (1988) . UNJ is the unweighted version from Gascuel (1997) .

Usage

NJ(x)

UNJ(x)

Arguments

x

A distance matrix.

Value

an object of class "phylo".

Details

NJ is a wrapper around nj from ape.

References

Gascuel O (1997). “Concerning the NJ algorithm and its unweighted version UNJ. 21 Pages 149-171 in: Mathematical hierarchies and biology. B. Mirkin, FR McMorris, 22 F. Roberts and A. Rzhetsky, eds.” American Mathematical Society, Providence, RI, 23.

Saitou N, Nei M (1987). “The Neighbor-Joining Method - a New Method for Reconstructing Phylogenetic Trees.” Molecular Biology and Evolution, 4(4), 406–425.

Studier JA, Keppler KJ (1988). “A Note on the Neighbor-Joining Algorithm of Saitou and Nei.” Molecular Biology and Evolution, 5(6), 729–731.

See also

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

Author

Klaus P. Schliep klaus.schliep@gmail.com

Examples

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