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.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {Overlapping Codon Model, Phylogenetic Clustering, and Alternative
           Partial Expectation Conditional Maximization Algorithm},
    author = {Wei-Chen Chen},
    journal = {Ph.D. Diss., Iowa Stat University},
    year = {2011},
  }