To cite stepwise in publications use:

Graham J, McNeney B and Seillier-Moiseiwitsch F (2005). Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics, 21:589-595

Corresponding BibTeX entry:

  @Article{,
    title = {Stepwise detection of recombination breakpoints in
      sequence alignments.},
    author = {J. Graham and B. McNeney and F. Seillier-Moiseiwitsch},
    journal = {Bioinformatics},
    volume = {21},
    year = {2005},
    pages = {589--595},
    url = {http://stat-db.stat.sfu.ca:8080/statgen/research/stepwise},
  }