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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},
  }

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They may not be fully stable and should be used with caution. We make no claims about them.