dnastring2kaks: dnastring2kaks

In kullrich/distSTRING: distSTRING calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Description

This function calculates Ka/Ks (pN/pS; according to Li (1993) or Nei and Gojobori (1986) for all combinations of a DNAStringSet.

Usage

dnastring2kaks(cds, model = "Li", threads = 1)

Arguments

cds	DNAStringSet coding sequence alignment [mandatory]
model	specify codon model either "Li" or "NG86" [default: Li]
threads	number of parallel threads [default: 1]

Value

A data.frame of KaKs values

Author(s)

Kristian K Ullrich

References

Nei and Gojobori. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol., 3(5), 418-426.

Ganeshan et al. (1997) Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virology. 71(1), 663-677.

Yang et al. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155(1), 431-449.

See Also

kaks

Examples

## load example sequence data
data("hiv", package="distSTRING")
#dnastring2kaks(hiv, model="Li")
hiv |> dnastring2kaks(model="Li")
#dnastring2kaks(hiv, model="NG86")
hiv |> dnastring2kaks(model="NG86")
#dnastring2kaks(hiv, model="NG86", threads=2)
hiv |> dnastring2kaks(model="NG86", threads=2)

kullrich/distSTRING documentation built on Dec. 21, 2021, 8:42 a.m.