Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates

Christensen Ole F.
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Christensen Ole F.: Bioinformatics Research Center, Aarhus University, Denmark

Statistical Applications in Genetics and Molecular Biology, 2006, vol. 5, issue 1, 31

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.

Keywords: EM-algorithm; Markov processes; maximum likelihood; pseudo-likelihood (search for similar items in EconPapers)
Date: 2006
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DOI: 10.2202/1544-6115.1217

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