compareCodons: compareCodons

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

compareCodons

Description

This function compares two codons and returns the number of syn and non-syn sites according to Nei and Gojobori (1986).

Usage

compareCodons(codA, codB)

Arguments

codA	codon A [mandatory]
codB	codon B [mandatory]

Value

vector of syn and non-syn sites

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

compareCodons("AAA","TTA")
compareCodons("AAA","TAT")
compareCodons("AAA","ATT")
compareCodons("AAA","TTT")
## load example sequence data
data("hiv", package="MSA2dist")
compareCodons(dnastring2codonmat(hiv)[1,1], dnastring2codonmat(hiv)[1,2])

kullrich/MSA2dist documentation built on April 26, 2024, 4:43 p.m.