Ziheng Yang
Abstract
Abstract This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous substitutions (dS and dN) between two protein-coding genes. Both the counting and maximum likelihood methods are included.
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Abstract This chapter discusses Markov chain models of amino acid replacement and codon substitution. It then discusses the various methods for estimating the numbers of synonymous and nonsynonymous substitutions (dS and dN) between two protein-coding genes. Both the counting and maximum likelihood methods are included.
Key concepts: Nonsynonymous substitution, Substitution (logic), Synonymous substitution, Amino acid substitution, Markov chain, Amino acid, Codon usage bias, Gene