Advances in Applied Probability
- Adv. in Appl. Probab.
- Volume 32, Number 2 (2000), 499-517.
Probabilistic models of DNA sequence evolution with context dependent rates of substitution
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.
Adv. in Appl. Probab. Volume 32, Number 2 (2000), 499-517.
First available in Project Euclid: 12 February 2002
Permanent link to this document
Digital Object Identifier
Mathematical Reviews number (MathSciNet)
Zentralblatt MATH identifier
Primary: 60J27: Continuous-time Markov processes on discrete state spaces
Secondary: 92D20: Protein sequences, DNA sequences 62E25
Jensen, Jens Ledet; Pedersen, Anne-Mette Krabbe. Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv. in Appl. Probab. 32 (2000), no. 2, 499--517. doi:10.1239/aap/1013540176. http://projecteuclid.org/euclid.aap/1013540176.