For an amino acid alignment, this relative entropy measures departure of the nongap empirical distribution in a column from the uniform distribution on the twenty standard amino acids.
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Multiple sequence alignment (MSA) is a bioinformatics technique used to align three or more biological sequences, which can be proteins, DNA, or RNA. The main goal of MSA is to identify similarities and differences among the sequences, enabling researchers to infer evolutionary relationships, functionally conserved regions, and structural features.