GERP++ (Genomic Evolutionary Rate Profiling) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint.
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PLoS Comput Biol. 2010 Dec 2;6(12):e1001025.
Identifying a high fraction of the human genome to be under selective constraint using GERP++.
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.