Maximum Composite Likelihood (Gamma Rates)

The Tamura-Nei (1993)Tamura_and_Nei_1993 distance with the gamma model estimated by the composite likelihood method (Tamura et al. 2004Tamura_et_al_2004) corrects for multiple hits, taking into account the different rates of substitution between nucleotides and the inequality of nucleotide frequencies.  In this distance, evolutionary rates among sites are modeled using the gamma distribution.  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. See related Tamura-Nei gamma distanceHC_Tamura_Nei_distance_with_Gamma_model.