Compute kaks for individual codon, the different mutations in a site will be considered as whole.
Usage
kaksCodon(seq_formated)
Arguments
seq_formated
Formated alignment sequence. i.e. the result after the treatment of DataFormatCorMut.
Value
A kaksCodon instance will be returned.
Details
Ka/Ks ratio was used as an indicator of selective pressure acting on a protein-coding gene. A Ka/Ks ratio of 1 indicates neutral selection, i.e., the observed ratio of non-synonymous mutations versus synonymous mutations exactly matches the ratio expected under a random mutation model. Thus, amino acid changes are neither being selected for nor against. A Ka/Ks value of <1 indicates="" negative="" selection="" pressure.="" that="" is="" to="" say="" most="" amino="" acid="" changes="" are="" deleterious="" and="" selected against,="" producing="" an="" imbalance="" in="" the="" observed="" mutations="" favors="" synonymous="" mutations.="" condition="" of="" ka="" ks="">1 , it indicates that amino acid changes are favored, i.e., they increase the organism's fitness. This unusual condition may reflect a change in the function of a gene or a change in environmental conditions that forces the organism to adapt. For example, highly variable viruses mutations which confer resistance to new antiviral drugs might be expected to undergo positive selection in a patient population treated with these drugs, such as HIV and HCV.
References
Chen, L., Perlina, A. & Lee, C. J. Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. Journal of virology 78, 3722-3732 (2004).