nucleotideDivergence: Nucleotide Divergence

In strataG: Summaries and Population Structure Analyses of Genetic Data

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).

Author(s)

Eric Archer [e-mail]

References

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

Examples

data(dloop.g)

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

strataG documentation built on Feb. 28, 2020, 9:07 a.m.