A number of different
Markov models of DNA sequence evolution have been proposed. These
substitution models differ in terms of the parameters used to describe the rates at which one
nucleotide replaces another during evolution. These models are frequently used in
molecular phylogenetic analyses. In particular, they are used during the calculation of likelihood of a tree (in
Bayesian and
maximum likelihood approaches to tree estimation) and they are used to estimate the evolutionary distance between sequences from the observed differences between the sequences.