In bioinformatics and evolutionary biology, a substitution matrix describes the rate at which one character in a sequence changes to other character states over time. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, where the similarity between sequences depends on their divergence time and the substitution rates as represented in the matrix.
Read more about Substitution Matrix: Background, Identity Matrix, Log-odds Matrices, Extensions and Improvements, Terminology
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