To cite phytools in publication use:

Revell LJ (2012). “phytools: An R package for phylogenetic comparative biology (and other things).” Methods in Ecology and Evolution, 3, 217-223.

As phytools is continually evolving, you may want to cite its version number. Find it with 'help(package=phytools)'.

Corresponding BibTeX entry:

  @Article{,
    title = {phytools: An R package for phylogenetic comparative
      biology (and other things).},
    author = {Liam J. Revell},
    journal = {Methods in Ecology and Evolution},
    year = {2012},
    volume = {3},
    pages = {217-223},
  }