phangorn: NJ – R documentation

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NJ

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 klaus.schliep@gmail.com

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.

Examples

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

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release

NJ