Covarion

The method of covarions, or concomitantly variable codons, is a technique in computational phylogenetics that allows the hypothesized rate of molecular evolution at individual codons in a set of nucleotide sequences to vary in an autocorrelated manner. Under the covarion model, the rates of evolution on different branches of a hypothesized phylogenetic tree vary in an autocorrelated way, and the rates of evolution at different codon sites in an aligned set of DNA or RNA sequences vary in a separate but autocorrelated manner. This provides additional and more realistic constraints on evolutionary rates versus the simpler technique of allowing the rate of evolution on each branch to be selected randomly from a suitable probability distribution such as the gamma distribution. Covarions is a concrete form of the more general concept of heterotachy.