K2P
A number of different Markov chain, 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 phylogenetics, molecular phylogenetic analyses. In particular, they are used during the calculation of likelihood of a tree (in Bayesian inference, 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. Introduction These models are phenomenological descriptions of the evolution of DNA as a string of four discrete states. These Markov models do not explicitly depict the mechanism of mutation nor the action of natural selection. Rather they describe the relative rates of different changes. For example, mutational biases and purifying selection favoring conservative ...
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Substitution Model
In biology, a substitution model, also called models of DNA sequence evolution, are Markov models that describe changes over evolutionary time. These models describe evolutionary changes in macromolecules (e.g., DNA sequences) represented as sequence of symbols (A, C, G, and T in the case of DNA). Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood estimation of phylogeny as well as Bayesian inference in phylogeny. Estimates of evolutionary distances (numbers of substitutions that have occurred since a pair of sequences diverged from a common ancestor) are typically calculated using substitution models (evolutionary distances are used input for distance methods such as neighbor joining). Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. Substitution models a ...
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