Estimation of point mutation rates is essential for studying molecular evolution and genetics. Point mutation rates are also important for developing tools for genome analyses, such as those used for homology searches (Altschul et al., 1990), sequence alignments (Katoh et al., 2002; Larkin et al., 2007), gene finding (Misawa and Kikuno, 2010), or detecting natural selection (Nei and Gojobori, 1986; Hughes and Nei, 1988; Yang, 2007; Yang and Nielsen, 2008), and for reconstructing phylogenetic trees (Felsenstein, 2004; Sullivan and Joyce, 2005). Patterns of mutations also affects the neutrality test for population genetics (Misawa and Tajima, 1997). According to the neutral theory (Kimura, 1968), new alleles may be produced at the same rate per individual as they are substituted in a population. On the basis of this theory, mutation rates were estimated from neutral substitution rates.