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- Title
A nucleotide substitution model with nearest-neighbour interactions.
- Authors
Lunter, Gerton; Hein, Jotun
- Abstract
It is well known that neighbouring nucleotides in DNA sequences do not mutate independently of each other. In this paper, we introduce a context-dependent substitution model and derive an algorithm to calculate the likelihood of sequences evolving under this model. We use this algorithm to estimate neighbour-dependent substitution rates, as well as rates for dinucleotide substitutions, using a Bayesian sampling procedure. The model is irreversible, giving an arrow to time, and allowing the position of the root between a pair of sequences to be inferred without using out-groups.
- Publication
Bioinformatics (Oxford, England), 2004, Vol 20 Suppl 1, pi216
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bth901