Scoring Function (also cost function or weight function)
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The methods used to evaluate the quality of the overlap between sequences. A variety of scoring functions are used to evaluate single replacement operations, multiple alignments (either whole or columns), and pairwise alignments. The score of an alignment of two sequences (a and b) is the sum of the score of all the replacement operations that lead from a to b. (http://www.netsci.org/Science/Bioinform/terms.html)
