title: Pseudo-likelihood for non-reversible nucleotide substitution models with neighbour dependent rates.
abstract: In the field of molecular evolution genome substitution models with neighbour dependent substitution rates have recently received much attention. It is well-known that substitution of nucleotides does not occur independently of neighbouring nucleotides, but there has been less focus on the phenomenon that this substitution process is also not time-reversible. In this paper I construct a pseudo-likelihood type method for inference in non-reversible substitution models with neighbour dependent substitution rates. I also construct an EM-algorithm for maximising the pseudo-likelihood. For human-mouse aligned sequence data a number of different models are investigated, where I show that strand-symmetric models are appropriate, and that overlapping di-nucleotide models do not fit the data well.
authors.affiliation: Bioinformatics Research Center, Aarhus University, Denmark. olefc@birc.au.dk
authors.forename: Ole F
authors.initials: OF
authors.lastname: Christensen
mesh_terms: D000465:Algorithms; D019943:Amino Acid Substitution / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D019143:Evolution, Molecular; D014644:Genetic Variation; D006801:Humans; D016013:Likelihood Functions; D008390:Markov Chains; D051379:Mice; D008957:Models, Genetic; D009711:Nucleotides / Q000032:analysis; D016415:Sequence Alignment
chemical_list: D009711:Nucleotides