Uniformization for Sampling Realizations of Markov Processes: Applications to Bayesian Implementations of Codon Substitution Models - LIRMM - Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier Access content directly
Journal Articles Bioinformatics Year : 2008

Uniformization for Sampling Realizations of Markov Processes: Applications to Bayesian Implementations of Codon Substitution Models

Abstract

MOTIVATION: Mapping character state changes over phylogenetic trees is central to the study of evolution. However, current probabilistic methods for generating such mappings are ill-suited to certain types of evolutionary models, in particular, the widely used models of codon substitution. RESULTS: We describe a general method, based on a uniformization technique, which can be utilized to generate realizations of a Markovian substitution process conditional on an alignment of character states and a given tree topology. The method is applicable under a wide range of evolutionary models, and to illustrate its usefulness in practice, we embed it within a data augmentation-based Markov chain Monte Carlo sampler, for approximating posterior distributions under previously proposed codon substitution models. The sampler is found to be more effcient than the conventional pruning-based sampler, with decorrelation times between draws from the posterior reduced by a factor of twenty or more. CONTACT: nicolas.rodrigue@umontreal.ca.

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Dates and versions

lirmm-00193706 , version 1 (04-12-2007)

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Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot. Uniformization for Sampling Realizations of Markov Processes: Applications to Bayesian Implementations of Codon Substitution Models. Bioinformatics, 2008, 24 (1), pp.56-62. ⟨10.1093/bioinformatics/btm532⟩. ⟨lirmm-00193706⟩
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