pegas (version 0.11)

mst: Minimum Spanning Tree and Network

Description

Computes a minimum spanning tree using Kruskal's algorithm, the minimum spanning network using Bandelt et al.'s algorithm, or the randomized minimum spanning tree (Paradis 2017).

Usage

mst(d)
msn(d)
rmst(d, B = 100)

Arguments

d

a distance matrix, either as an object of class "dist", or a (square symmetric) matrix.

B

number of randomizations.

Value

an object of class "haploNet".

References

Bandelt, H. J., Forster, P. and Rohl, A. (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37--48.

Kruskal, J. B., Jr. (1956) On the shortest spanning subtree of a graph and the traveling salesman problem. Proceedings of the American Mathematical Society, 7, 48--50.

Paradis, E. (2018) Analysis of haplotype networks: the randomized minimum spanning tree method. Methods in Ecology and Evolution, 9, 000--000. DOI: 10.1111/2041-210X.12969.

See Also

haploNet, mjn

Examples

# NOT RUN {
data(woodmouse)
d <- dist.dna(woodmouse, "n")
(r <- mst(d))
plot(r)
# }