To cite TransPhylo:

  Didelot et al (2017). Genomic infectious disease epidemiology in
  partially sampled and ongoing outbreaks.

A BibTeX entry for LaTeX users is

  @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},
  }