%0 Journal Article %1 jensen2000probabilistic %A Jensen, Jens Ledet %A Pedersen, Anne-Mette Krabbe %D 2000 %I Applied Probability Trust %J Advances in Applied Probability %K MCMC context-dependent-mutation data_augmentation %N 2 %P 499--517 %R 10.1239/aap/1013540176 %T Probabilistic models of DNA sequence evolution with context dependent rates of substitution %U http://dx.doi.org/10.1239/aap/1013540176 %V 32 %X 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.

@article{jensen2000probabilistic, 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. }, added-at = {2014-06-03T16:13:32.000+0200}, ajournal = {Adv. in Appl. Probab.}, author = {Jensen, Jens Ledet and Pedersen, Anne-Mette Krabbe}, biburl = {https://www.bibsonomy.org/bibtex/23592991275b1d2976193e274eaa3375d/peter.ralph}, doi = {10.1239/aap/1013540176}, interhash = {65917314d6e65bd559ea6000d54d6dba}, intrahash = {3592991275b1d2976193e274eaa3375d}, journal = {Advances in Applied Probability}, keywords = {MCMC context-dependent-mutation data_augmentation}, month = {06}, number = 2, pages = {499--517}, publisher = {Applied Probability Trust}, timestamp = {2014-06-03T16:13:32.000+0200}, title = {Probabilistic models of {DNA} sequence evolution with context dependent rates of substitution}, url = {http://dx.doi.org/10.1239/aap/1013540176}, volume = 32, year = 2000 }