To cite phyclust in a publication use:

Chen, W.-C. (2011) Overlapping Codon model, Phylogenetic Clustering, and Alternative Partial Expectation Conditional Maximization Algorithm, Ph.D. Diss., Iowa Stat University.

Corresponding BibTeX entry:

  @Manual{,
    title = {Overlapping Codon Model, Phylogenetic Clustering, and
      Alternative Partial Expectation Conditional Maximization
      Algorithm},
    author = {{Chen} and {W.-C.}},
    journal = {Ph.D. Diss., Iowa Stat University},
    year = {2011},
    url = {http://thirteen-01.stat.iastate.edu/snoweye/phyclust/},
  }