number of generations for natural selection to "weed out" deleterious mutations from a population, especially if their effect on fitness is weak. This limits the usefulness of the Ka/Ks ratio for comparing closely related populations. Individual codon approach Additional information can be gleaned by determining the Ka/Ks ratio at specific codons within a gene sequence. For instance, the frequency-tuning region of an opsin may be under enhanced selective pressure when a species colonises and adapts to new environment, whereas the region responsible for initializing a nerve signal may be under purifying selection. In order to detect such effects, one would ideally calculate the Ka/Ks ratio at each site. However this is computationally expensive and in practise, a number of Ka/Ks classes are established, and each site is assigned to the best-fitting class. The first step in identifying whether positive selection acts on sites is to compare a test where the Ka/Ks ratio is constrained to be < 1 in all sites to one where it may take any value, and see if permitting Ka/Ks to exceed 1 in some sites improves the fit of the model. If this is the case, then sites fitting into the class where Ka/Ks > 1 are candidates to be experiencing positive selection. This form of test can either identify sites that further laboratory research can examine to determine possible selective pressure; or, sites believed to have functional significance can be assigned into different Ka/Ks classes before the model is run. Notes References Further reading External links KaKs_Calculator Free online server tool that calculates KaKs ratios among multiple sequences SeqinR: A free and open biological sequence analysis package for the R language that includes KaKs calculation Molecular evolution Genetics Statistical ratios