Skip to main content Accessibility help

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

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


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.


Corresponding author

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


Hide All
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368376.
Felsenstein, J. and Churchill, G. (1996). A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13, 93104.
Geyer, C. J. (1996). Likelihood inference for spatial point processes. In Proc. Seminaire Europeen de Statistique, Stochastic Geometry, Likelihood and Computation, eds Barndorff-Nielsen, O., Kendall, W. S. and van Lieshout, M. N. M. Chapman and Hall, New York.
Goldman, N. (1993). Statistical tests of models of DNA substitutions. J. Mol. Evol. 36, 182198.
Goldman, N. and Yang, Z. (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725736.
Von Haeseler, A. and Schöniger, M. (1998). Evolution of DNA or amino acid sequences with dependent sites. J. Comp. Biol. 5, 149163.
Kypr, J., Mrazek, J. and Reich, J. (1989). Nucleotide composition bias and CpG dinucleotide content in the genomes of HIV and HTLV 1/2. Biochim. Biophys. Acta 1009, 280282.
Muse, S. V. and Gaut, B. S. (1994). A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11, 715724.
Pedersen, A. K., Wiuf, C. and Christiansen, F. B. (1998). A codon-based model designed to describe lentiviral evolution. Mol. Biol. Evol. 15, 10691081.
Thorne, J., Kishino, H. and Felsenstein, J. (1991). An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33, 114124.
Yang, Z. (1993). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites. Mol. Biol. Evol. 10, 13961401.


MSC classification


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed