strataG (version 2.4.905)

variableSites: Variable Sites

Description

Identify variable sites among sequences.

Usage

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

Arguments

x

a '>gtypes object with sequences, a DNAbin object, or a list of sequences.

bases

character vector of bases to consider.

simplify

if there is a single locus, return result in a simplified form? If FALSE a list will be returned wth one element per locus.

Value

A list with:

site

a DNAbin object composed of variable sites.

site.freqs

a matrix of base pair frequencies by site.

See Also

fixedSites

Examples

# NOT RUN {
data(dolph.haps)

variableSites(dolph.haps)

# }