seg.sites {ape}R Documentation

Find Segregating Sites in DNA Sequences

Description

This function gives the indices of segregating (polymorphic) sites in a sample of DNA sequences.

Usage

seg.sites(x)

Arguments

x a matrix or a list which contains the DNA sequences.

Details

If the sequences are in a list, all the sequences must be of the same length.

Value

A numeric vector giving the indices of the segregating sites.

Note

The present version looks for the sites which are ``variable'' in the data in terms of different letters. This may give unexpected results if there are ambiguous bases in the data.

Author(s)

Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr

See Also

base.freq, GC.content, theta.s, nuc.div

Examples

data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)

[Package ape version 2.3 Index]