R: Test of the Neutral Mutation Hypothesis

tajima.test {pegas} | R Documentation

## Test of the Neutral Mutation Hypothesis

### Description

This function tests the neutral mutation hypothesis with Tajima's D.

### Usage

    tajima.test(x)

### Arguments

`x` | a set of DNA sequences (object of class `"DNAbin"`).

### Value

A list with three numeric values:

`D` | Tajima's D statistic.
`Pval.normal` | the p-value assuming that D follows a normal distribution with mean zero and variance one.
`Pval.beta` | the p-value assuming that D follows a beta distribution after rescaling on [0, 1] (Tajima, 1989).

### Note

Alignment gaps in the sequences are ignored when calculating pairwise distances.

### Author(s)

Emmanuel Paradis

### References

Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 595–595.

### Examples

    require(ape)
    data(woodmouse)
    tajima.test(woodmouse)

[Package pegas version 1.1 Index]