The Tamura-Nei (1993) distance with the gamma model estimated by the composite likelihood method (Tamura 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 for computing this distance. See related Tamura-Nei gamma distance.