Data from: Accurate estimation of substitution rates with neighbour-dependent models in a phylogenetic context

Jean Bérard & Laurent Guéguen
Most models and algorithms developed to perform statistical inference from DNA data make the assumption that substitution processes affecting distinct nucleotide sites are stochastically independent. This assumption ensures both mathematical and computational tractability, but is in disagreement with observed data in many situations -- one well-known example being CpG dinucleotide hypermutability in mammalian genomes. In this paper, we consider the class of RN95+YpR substitution models, which allows neighbour-dependent effects -- including CpG hypermutability -- to...
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