Tamura 3 parameter (Gamma rates and Heterogeneous patterns)

Tamura’s 3-parameter model corrects for multiple hits, taking into account the differences in transition A transition occurs when a purine is substituted by a purine, or a pyrimidine by a pyrimidine.RH_Transitional and transversion A change from a purine to a pyrimidine, or vice versa, is a transversion.RH_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 parameter According to the gamma distribution, the substitution rate often varies from site to site within a sequence. The shape of this distribution is determined by a value known as the gamma parameter, which is also known as the shape parameter.RH_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:

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 According to the gamma distribution, the substitution rate often varies from site to site within a sequence. The shape of this distribution is determined by a value known as the gamma parameter, which is also known as the shape parameter., and

The variances can be estimated by the bootstrap method.