seg.sites: Find Segregating Sites in DNA Sequences

In gjuggler/ape: Analyses of Phylogenetics and Evolution

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. Ambiguous nucleotides are ignored.

Value

A numeric (integer) 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

See Also

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

Examples

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

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.