  The presence of neighbor dependencies generated a specific pattern of
dinucleotide frequencies in all organisms. Especially, the
CpG-methylation-deamination process is the predominant substitution process in
vertebrates and needs to be incorporated into a more realistic model for
nucleotide substitutions. Based on a general framework of nucleotide
substitutions we develop a method that is able to identify the most relevant
neighbor dependent substitution processes, measure their strength, and judge
their importance to be included into the modeling. Starting from a model for
neighbor independent nucleotide substitution we successively add neighbor
dependent substitution processes in the order of their ability to increase the
likelihood of the model describing given data. The analysis of neighbor
dependent nucleotide substitutions in human, zebrafish and fruit fly is
presented. A web server to perform the presented analysis is publicly
available.
