Computes a neighborNet from a distance matrix

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.

Value

neighborNet returns an object of class networx.

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.

References

Bryant D, Huson DH (2023). “NeighborNet: improved algorithms and implementation.” Frontiers in bioinformatics, 3, 1178600. doi:10.3389/fbinf.2023.1178600 .

Bryant D, Moulton V (2004). “Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks.” Molecular Biology and Evolution, 21(2), 255-265. doi:10.1093/molbev/msh018 .

See also

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

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

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

plot(nnet, type="outline")