Maximum Composite Likelihood (Gamma Rates and Heterogeneous Patterns)

The Tamura-Nei (1993) distance estimated by the composite likelihood method (Tamura et al. 2004) with the gamma model corrects for multiple hits, taking into account the rate substitution differences 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 for computing this distance. When the nucleotide frequencies between the sequences are different, the expected proportions of observed differences (P1, P2, and Q) in the computation of the composite likelihood can be obtained by the modified formulas according to Tamura and Kumar (2002) to relax the assumption of the substitution pattern homogeneity.