title: Phylogenetic distances for neighbour dependent substitution processes.
abstract: 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. In the simplest non-trivial case of a Jukes-Cantor model with CpG influence, we provide and justify mathematically consistent estimators in these two settings. We also provide asymptotic confidence intervals, valid for nucleotidic sequences of finite length, and we compute explicit formulas for the estimators and for their confidence intervals. In the general case of an RN model with YpR influence, we extend these results under a proviso, namely that the equation defining the estimator has a unique solution.
authors.affiliation: Université Joseph Fourier Grenoble 1, Institut Fourier UMR 5582 UJF-CNRS, 100 rue des Maths, BP 74, 38402 Saint Martin d'Hères, France. mikael.falconnet@ujf-grenoble.fr
authors.forename: Mikael
authors.initials: M
authors.lastname: Falconnet
mesh_terms: D000465:Algorithms; D000704:Analysis of Variance; D001483:Base Sequence / Q000235:genetics; D003198:Computer Simulation; D016001:Confidence Intervals; D018899:CpG Islands / Q000235:genetics; D019143:Evolution, Molecular; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny; D017354:Point Mutation / Q000235:genetics*; D016415:Sequence Alignment; D013997:Time Factors