STEC Center BannerLink to STEC HomepageLink to NFSTC Homepage
About STEC Center
  • Advisory Committee
  • Investigators and Strains
  • Clonal Analysis of STEC
  • Contact us
  • Databases
  • Isolate Database
  • EcMLST System
  • Literature Database
  • Tools
  • Obtain Strains
  • Reference Strain Sets
  • Molecular Protocols
  • Computer Programs
  • Server Statistics (Internal)
  • About the website
  • Accessibility
  • Privacy notice
  • Disclaimer
  • Sponsor
  • Stephens - Analysis of clustered polymorphisms

    Sample In | Sample Out | Download (31.7 KB Zip File)
    Instructions

    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.

    Contact stec@cvm.msu.edu
    Operated by Shannon D. Manning at Michigan State University