CodonRates is a program to estimate divergence times and `absolute rates' of synonymous and nonsynonymous substitution with protein-coding genes. The conventional programs, such as PAML (Yang 1997), HYPHY (Kosakovsky Pond and Muse 2000), can estimate the `amounts' of nonsynonymous and synonymous substitution and their ratio, but fail to separate evolutionary amounts into times and rates without using molecular clock. By adopting Bayesian framework, CodonRates can separate the evolutionary amount into time and synonymous and nonsynonymous rates without using molecular clock. Other information than sequence data, such as fossil constraints and prior distribution for the root time, are required.
For the application of CodonRates, see Seo et al. (2004, Mol. Biol. Evol. 21:1201-1213, [pdf]). For more general things about Bayesian estimation of divergence times, see Thorne et al. (1998, Mol. Biol. Evol. 15:1647-1657), Kishino et al. (2001, Mol. Biol. Evol. 18:352-361) and Thorne and Kishino (2002, Syst. Biol. 51:689-702).