R: dN/dS Ratio

dnds {ape} | R Documentation

## dN/dS Ratio

### Description

This function computes the pairwise ratios dN/dS for a set of aligned DNA sequences using Li's (1993) method.

### Usage

    dnds(x, code = 1, codonstart = 1, quiet = FALSE)

### Arguments

`x` | an object of class `"DNAbin"` (matrix or list) with the aligned sequences.
`code` | an integer value giving the genetic code to be used. Currently only 1 (standard code) and 2 (vertebrate mitochondrial code) are supported.
`codonstart` | an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence.
`quiet` | single logical value: whether to indicate progress of calculations.

### Value

an object of class `"dist"`.

### Author(s)

Emmanuel Paradis

### References

Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36, 96–99.

### See Also

`AAbin`, `trans`, `alview`

### Examples

    data(woodmouse)
    res <- dnds(woodmouse, quiet = TRUE) # NOT correct
    res2 <- dnds(woodmouse, code = 2, quiet = TRUE) # using the correct code
    identical(res, res2)

[Package ape version 5.4 Index]