replaced in the mutation, and the replacement amino acid. The PAM matrices are a mathematical tool that account for these varying rates of acceptance when evaluating the similarity of proteins during alignment.

Terminology

The term accepted point mutation was initially used to describe the mutation phenomenon. However, the acronym PAM was preferred over APM due to readability, and so the term point accepted mutation is used more regularly. Because the value in the PAM_n matrix represents the number of mutations per

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