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A nucleotide substitution model with nearest-neighbour interactions.

Abstract:

MOTIVATION: 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 al...

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Publication status:
Published

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Journal:
Bioinformatics (Oxford, England)
Volume:
20 Suppl 1
Issue:
SUPPL. 1
Pages:
i216-i223
Publication date:
2004-08-05
DOI:
EISSN:
1367-4811
ISSN:
1367-4803
URN:
uuid:a79598b5-8e8d-4b81-a721-c366199258d5
Source identifiers:
68319
Local pid:
pubs:68319

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