Inference of Natural Selection from Interspersed Genomically coHerent elemenTs

http://compgen.bscb.cornell.edu/INSIGHT/

 INSIGHT is a method for inferring signatures of recent natural selectionfrom patterns of polymorphism and divergence across a collection of short dispersed genomic elements. The core of the method is a full probabilistic model that allows it to make use of sequence data across a dispersed set of elements to disentangle the effects of neutral genetic drift from positive, strong negative, and weak negative selection. INSIGHT provides estimates of three main measures: the fraction of nucleotides under selection (ρ), the number of divergences driven by positive selection (D_p), and the number of polymorphisms under weak negative selection (P_w). Maximum likelihood inference is achieved through an EM algorithm (INSIGHT-EM) implemented in C.