To cite PhylogeneticEM in publications use:

  Paul Bastide, Mahendra Mariadassou & Stephane Robin (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 doi:10.1111/rssb.12206.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree}},
    author = {Paul Bastide and Mahendra Mariadassou and Stephane 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 = {https://doi.org/10.1111/rssb.12206},
  }