strataG (version 2.4.905)

nucleotideDiversity: Nucleotide Diversity

Description

Calculate nucleotide diversity for set of haplotypes.

Usage

nucleotideDiversity(x, bases = c("a", "c", "g", "t"), simplify = TRUE)

Arguments

x

a set of sequences or a '>gtypes object with sequences.

bases

nucleotides to consider when calculating diversity.

simplify

if TRUE and only one loci exists, return a vector, otherwise, a list of vectors with one element per locus will be returned.

Value

Vector of nucleotide diversity by site.

Examples

# NOT RUN {
data(dloop.g)

nd <- nucleotideDiversity(dloop.g)
quantile(nd)

# }