Software

► CodonRates

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).

 

► You can do the following analysis with CodonRates (example).

--- The divergence times and synonymous and nonsynonymous substitution rates of mammalian mitochondrial protein-coding genes (Seo et al. 2008 Proceedings of the Institute of Statistical Mathematics. 56(1):37-54). ---

Divergence times (posterior medians and 95% credibility intervals) of mammalian species were estimated with 12 protein-coding genes (first figure).  In the second – fourth figures, I show the posterior medians of synonymous (red balls) and nonsynonymous (blue balls) rates and omega’s (pink balls) of Cox1.  The bigger is the ball, the higher is the evolutionary rate or omega.  The following figures were generated with CodonRates.

       　　

 

You can see how synonymous and nonsynonymous rates and omega’s change over time.  The following figures were generated by Mathematica (Ver. 4.0) with the results of CodonRates.

  

 

 

► Download:    CodonRates 1.0        User’s guide

 

Any suggestions or inquires about this program would be appreciated. 

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