|Stephens - Analysis of clustered polymorphisms
Sample In | Sample Out | Download (31.7 KB Zip File)
STEPHENS is based on the method of Clay Stephens (1985) in Mol. Biol. Evol. 2:539-556. The program classifies each polymorphic site by how it groups (or partitions) the sequences and determines the probability that the sites supporting a give partition are clustered. The test statistics are d(0) and g(0) which are defined in Stephens' paper. STEPHENS reads a list of polymorphic sites and their locations in a collection of DNA sequences, tabulates the sites that support various phylogenetic partitions, and then performs two exact tests for clustering of polymorphic sites.