To cite outbreaker:

T J, A C, X D, S C, C F, N F (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},
  }