ape (version 1.8-4)

nuc.div: Nucleotide Diversity

Description

This function computes the nucleotide diversity from a sample of DNA sequences.

Usage

nuc.div(x, variance = FALSE, pairwise.deletion = FALSE)

Value

A numeric vector with one or two values (if variance = TRUE).

Details

The nucleotide diversity is the sum of the number of differences between pairs of sequences divided by the number of comparisons (i.e. n(n - 1)/2, where n is the number of sequences).

The variance of the estimated diversity uses formula (10.9) from Nei (1987). This applies only if all sequences are of the same lengths, and cannot be used if pairwise.deletion = TRUE. A bootstrap estimate may be in order if you insist on using the latter option.

References

Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.

See Also

base.freq, GC.content, theta.s, seg.sites

Examples

data(woodmouse)
nuc.div(woodmouse)
nuc.div(woodmouse, TRUE)
nuc.div(woodmouse, FALSE, TRUE)