R: Find Segregating Sites in DNA Sequences

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. Ambiguous nucleotides are ignored.

### Value

A numeric (integer) vector giving the indices of the segregating sites.

### Author(s)

Emmanuel Paradis

### See Also

`base.freq`, `theta.s`, `nuc.div`

### Examples

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

[Package ape version 5.0 Index]