Interpreting Results
The dN/dS ratio is used to infer the direction and magnitude of natural selection acting on protein coding genes. A ratio greater than one implies positive or Darwinian selection; less than one implies purifying (stabilizing) selection; and a ratio of one indicates neutral (i.e. no) selection. However, a combination of positive and purifying selection at different points within the gene or at different times along its evolution may cancel each other out, giving an average value that may be lower, equal or higher than one.
Of course, it is necessary to perform a statistical analysis to determine whether a result is significantly different from one, or whether any apparent difference may occur as a result of a limited data set. The appropriate statistical test for an approximate method involves approximating dN − dS with a normal approximation, and determining whether zero falls within the central region of the approximation. More sophisticated likelihood techniques can be used to analyse the results of a Maximum Likelihood analysis, by performing a chi-square test to distinguish between a null model (dN/dS = 1) and the observed results.
Read more about this topic: Ka/Ks Ratio
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