seg.sites

0th

Percentile

Find Segregating Sites in DNA Sequences

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

Keywords
univar
Usage
seg.sites(x)
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.

See Also

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

Aliases
Examples
data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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