neighborNet: Computes a neighborNet from a distance matrix

In phangorn: Phylogenetic Reconstruction and Analysis

Computes a neighborNet from a distance matrix

Description

Computes a neighborNet, i.e. an object of class networx from a distance matrix.

Usage

neighborNet(x, ord = NULL)

Arguments

x	a distance matrix.
ord	a circular ordering.

Details

neighborNet is still experimental. The cyclic ordering sometimes differ from the SplitsTree implementation, the ord argument can be used to enforce a certain circular ordering.

Value

neighborNet returns an object of class networx.

Author(s)

Klaus Schliep [e-mail]

References

Bryant, D. & Moulton, V. (2004) Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks. Molecular Biology and Evolution, 2004, 21, 255-265

See Also

splitsNetwork, consensusNet, plot.networx, lento, cophenetic.networx, distanceHadamard

Examples

data(yeast)
dm <- dist.ml(yeast)
nnet <- neighborNet(dm)
plot(nnet)

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