A substitution matrix assigns a score to aligning each pair of sequence symbols. Scores based on logarithms of observed-to-background pair frequencies turn products of relative support into additive alignment scores.
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A substitution matrix is a mathematical tool used primarily in bioinformatics to score alignments of biological sequences, such as DNA, RNA, or protein sequences. It quantifies the likelihood of one character (nucleotide or amino acid) being replaced by another during the evolution of organisms.