Tamura 3 parameter (Gamma rates and Heterogeneous patterns)

Tamura’s 3-parameter model corrects for multiple hits, taking into account the differences in transitionRH_Transitional and transversionRH_Transversional rates and the G+C-content bias (1992Tamura_1992).  Evolutionary rates among sites are modeled using the gamma distribution, and you will need to provide a gamma parameterRH_Gamma_parameter for computing this distance. When the G+C-contents between the sequences are different, the modified formula (Tamura and Kumar 2002Tamura_and_Kumar_2002) relaxes the assumption of substitution pattern homogeneity.

 

The Tamura 3-parameter model

 

MEGA provides facilities for computing the following quantities:

Quantity

Description

d: Transitions & Transversions

Number of nucleotide substitutions per site.

s: Transitions only

Number of transitional substitutions per site.

v: Transversions only

Number of transversional substitutions per site.

R = s/v

Transition/transversion ratio.

L: No of valid common sites

Number of sites compared.

 

Formulas for computing these quantities are as follows:

Distances

where P and Q are the proportion of sites with transitional and transversional differences, respectively, a is the gamma parameter, and

The variances can be estimated by the bootstrap method.