To cite TransPhylo:

Didelot, Xavier, Fraser, Christophe, Gardy, Jennifer, Colijn, Caroline (2017). “Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks.” Molecular Biology and Evolution, 34, 997–1007. doi:10.1093/molbev/msw275, https://academic.oup.com/mbe/article/34/4/997/2919386.

Corresponding BibTeX entry:

  @Article{,
    title = {Genomic infectious disease epidemiology in partially
      sampled and ongoing outbreaks},
    author = {{Didelot} and {Xavier} and {Fraser} and {Christophe} and
      {Gardy} and {Jennifer} and {Colijn} and {Caroline}},
    journal = {Molecular Biology and Evolution},
    doi = {10.1093/molbev/msw275},
    pages = {997--1007},
    url = {https://academic.oup.com/mbe/article/34/4/997/2919386},
    volume = {34},
    year = {2017},
  }