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.

Submitted: March 28, 2006 · Accepted: June 27, 2006 · Published: July 31, 2006

Recommended Citation

Christensen, Ole F. (2006) "Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates," Statistical Applications in Genetics and Molecular Biology: Vol. 5 : Iss. 1, Article 18.
Available at: http://www.bepress.com/sagmb/vol5/iss1/art18