Accurate estimations of evolutionary times in the context of strong CpG hypermutability.

We consider the substitution model T92+CpG of DNA sequence evolution which takes into account the hypermutability of CpG dinucleotides, an effect that can be especially observed in vertebrate genomes. We provide an exact method to simulate the evolution of finite DNA sequences under this model and numerical procedures to infer evolutionary times in two cases: between an ancestral and a present sequence and between two homologous sequences. We show on simulated data that our new numerical method yields very accurate estimations of divergence times.

Priors for the Bayesian star paradox.

We show that the Bayesian star paradox, first proved mathematically by Steel and Matsen for a specific class of prior distributions, occurs in a wider context including less regular, possibly discontinuous, prior distributions.

Phylogenetic distances for neighbour dependent substitution processes.

We consider models of nucleotidic substitution processes where the rate of substitution at a given site depends on the state of the neighbours of the site. We first estimate the time elapsed between an ancestral sequence at stationarity and a present sequence. Second, assuming that two sequences are issued from a common ancestral sequence at stationarity, we estimate the time since divergence.