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, strict = FALSE, trailingGapsAsN = TRUE)

### Arguments

`x` | a matrix or a list which contains the DNA sequences.
`strict` | a logical value; if `TRUE`, ambiguities and gaps in the sequences are not interpreted in the usual way.
`trailingGapsAsN` | a logical value; if `TRUE` (the default), the leading and trailing alignment gaps are considered as unknown bases (i.e., N).

### Details

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

If `strict = FALSE` (the default), the following rule is used to determine if a site is polymorphic or not in the presence of ambiguous bases: ‘A’ and ‘R’ are not interpreted as different, ‘A’ and ‘Y’ are interpreted as different, and ‘N’ and any other base (ambiguous or not) are interpreted as not different. If `strict = TRUE`, all letters are considered different.

Alignment gaps are considered different from all letters except for the leading and trailing gaps if `trailingGapsAsN = TRUE` (which is the default).

### Value

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

### Author(s)

Emmanuel Paradis

### See Also

`base.freq`, `theta.s`, `nuc.div` (last two in pegas)

### Examples

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

[Package ape version 5.6-2 Index]