strataG (version 1.0.3)

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.

References

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

Examples

data(dolph.strata)
data(dolph.seqs)
strata <- dolph.strata$fine
names(strata) <- dolph.strata$ids
dloop <- sequence2gtypes(dolph.seqs, strata, seq.names = "dLoop")

nucleotideDivergence(dloop)