A Scoring Function maps an abstract concept to a numeric value. A variety of scoring functions are used to evaluate ("score") single edit operations (or simply the combination of characters involved), columns of a multiple alignment, whole pairwise alignments, and whole multiple alignments. Generally, the score of an alignment of two sequences s and t is the sum of the score of all its edit operations that lead from s to t. For multiple alignment, there are various competing ways to calculate a score, e.g. sum-of-pairs score, or scoring along a tree. Usually, the terms Cost Function and Weight Function can be treated as synonyms, although they carry the idea that "small values are desirable". Both similarity measure and distance measure are specific type's of a scoring function.
Cost Function Weight Function score