Abstract
This chapter describes methods for estimating total number of nucleotide substitutions. The initiation and termination codons are excluded from the comparison, because the former is usually invariant and changes of the latter are quite restrictive. When the number of differences varies depending on the types of base pairs, and furthermore when the value of K is expected to become more than 1.0, the four- and six-parameter methods are more suitable than other methods. In particular, the estimate obtained by the six-parameter method is often close to the true value even though the value of K becomes much larger. The formula for the six-parameter method, however, frequently tends to become inapplicable owing to sampling and stochastic errors unless the DNA sequences compared are sufficiently long. If the number of nucleotide differences between two DNA sequences is very small, the number of synonymous and nonsynonymous substitutions can be obtained simply by counting synonymous and nonsynonymous nucleotide differences.