strataG (version 2.4.905)

nucleotideDivergence: Nucleotide Divergence

Description

Calculate Nei's dA between strata, and distributions of between- and within-strata nucleotide divergence (sequence distance).

Usage

nucleotideDivergence(g, probs = c(0, 0.025, 0.5, 0.975, 1), model = "raw", ...)

Arguments

g

a '>gtypes object.

probs

a numeric vector of probabilities of the pairwise distance distributions with values in 0:1.

model

evolutionary model to be used. see dist.dna for options.

...

other arguments passed to dist.dna.

Value

a list with summaries of the within and between strata pairwise distances including Nei's dA (in between).

References

Nei, M., and S. Kumar (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Oxford. (dA: pp. 256, eqn 12.67)

Examples

# NOT RUN {
data(dloop.g)

nd <- nucleotideDivergence(dloop.g)
nd$within
nd$between

# }