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Computational Molecular Evolution$
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Ziheng Yang

Print publication date: 2006

Print ISBN-13: 9780198567028

Published to Oxford Scholarship Online: April 2010

DOI: 10.1093/acprof:oso/9780198567028.001.0001

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Models of amino acid and codon substitution

Models of amino acid and codon substitution

(p.40) 2 Models of amino acid and codon substitution
Computational Molecular Evolution


Oxford University Press

Chapter 1 discussed continuous-time Markov chain models of nucleotide substitution and their application to estimate the distance between two nucleotide sequences. This chapter discusses similar Markov chain models to describe substitutions between amino acids in proteins or between codons in protein-coding genes. It makes straightforward use of the Markov chain theory introduced in Chapter 1, except that the states of the chain are now the 20 amino acids or the 61 sense codons (in the universal genetic code), instead of the four nucleotides. Exercises are provided at the end of the chapter.

Keywords:   Markov chain models, amino acid replacement, codon substitution, protein sequences

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