To cite outbreaker2:

Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N (2014). “Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data.” PLoS Computational Biology, 10(11), e1003457. doi:10.1371/journal.pcbi.1003457.

Corresponding BibTeX entry:

  @Article{,
    title = {Bayesian reconstruction of disease outbreaks by combining
      epidemiologic and genomic data},
    journal = {PLoS Computational Biology},
    year = {2014},
    author = {Thibaut Jombart and Anne Cori and Xavier Didelot and
      Simon Cauchemez and Christophe Fraser and Neil Ferguson},
    volume = {10},
    number = {11},
    pages = {e1003457},
    doi = {10.1371/journal.pcbi.1003457},
  }