Hotel Estoril Eden, Monte Estoril,
5-8 October 2005



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seudo-Likelihood for the General Nucleotide Substitution Model with Neighbour Dependent Rates

Ole Christensen
Aarhus University, Denmark

In the field of molecular evolution Markov processes with neighbour dependent substitution rates have recently received much interest. It is well-known that substitution of  nucleotides are not occurring independently of neighbouring nucleotides, but there has been less focus on the phenomenon that this substitution process is also not reversible. We construct a pseudo-likelihood type method for inference in the general Markov process model with neighbour dependent substitution rates, which was introduced by Hwang and Green. We also construct an EM-algorithm for maximising the pseudo-likelihood.