# 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*.

###

###

###

###

### Any suggestions or inquires about this program would be appreciated.

### (contact : )

###

###