To cite phytools in publication use:

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3 217-223. doi:10.1111/j.2041-210X.2011.00169.x

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},
  }