To cite PhylogeneticEM in publications use:

Bastide P, Mariadassou M, Robin S (2017). “Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree.” Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4), 1067–1093. ISSN 1467-9868, doi: 10.1111/rssb.12206, http://onlinelibrary.wiley.com/doi/10.1111/rssb.12206/full.

Corresponding BibTeX entry:

  @Article{,
    title = {{Detection of adaptive shifts on phylogenies by using
      shifted stochastic processes on a tree}},
    author = {Paul Bastide and Mahendra Mariadassou and St├ęphane
      Robin},
    journal = {Journal of the Royal Statistical Society: Series B
      (Statistical Methodology)},
    month = {sep},
    year = {2017},
    volume = {79},
    number = {4},
    issn = {1467-9868},
    pages = {1067--1093},
    doi = {10.1111/rssb.12206},
    url = {http://onlinelibrary.wiley.com/doi/10.1111/rssb.12206/full},
  }