Models of amino acid and codon substitution
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.
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