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Probabilistic models of DNA sequence evolution with context dependent rates of substitution

  • Jens Ledet Jensen (a1) and Anne-Mette Krabbe Pedersen (a1)

Abstract

We consider Markov processes of DNA sequence evolution in which the instantaneous rates of substitution at a site are allowed to depend upon the states at the sites in a neighbourhood of the site at the instant of the substitution. We characterize the class of Markov process models of DNA sequence evolution for which the stationary distribution is a Gibbs measure, and give a procedure for calculating the normalizing constant of the measure. We develop an MCMC method for estimating the transition probability between sequences under models of this type. Finally, we analyse an alignment of two HIV-1 gene sequences using the developed theory and methodology.

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Corresponding author

Postal address: Department of Theoretical Statistics, Institute of Mathematics, Ny Munkegade, DK-8000 Aarhus C, Denmark. Email address: jlj@imf.au.dk
∗∗ Postal address: Department of Genetics and Ecology, Institute of Biological Sciences, Ny Munkegade, DK-8000 Aarhus C, Denmark. Email address: annemet@imf.au.dk

References

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