To cite outbreaker:

Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N (accepted). Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Computational Biology.

Corresponding BibTeX entry:

  @Article{,
    title = {Bayesian reconstruction of disease outbreaks by combining
      epidemiologic and genomic data},
    journal = {PLoS Computational Biology},
    year = {accepted},
    author = {Jombart T and Cori A and Didelot X and Cauchemez S and
      Fraser C and Ferguson N},
  }