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  • 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.

    Operated by Shannon D. Manning at Michigan State University