Using evolutionary algorithms in finding of optimized nucleotide substitution matrices

Mutations occurring in biological DNA sequences are not completely random but are a result of coevolution between mutational pressure with selection constraints around the genetic code [2, 5] and can be optimized to some extent during evolution ([6]). On one hand, most mutations are deleterious and generate energetic costs of their repairing, therefore a tendency to decrease the mutation rate should exist. On the other hand, mutations are responsible for genetic diversity, which is necessary for adaptation in changing environment. Therefore, an elevated level of mutation rate should be also expected in these cases. It indicates that the real mutational pressure should be subjected to some optimization in biological systems.