To cite phangorn in a publication use:

Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

As phangorn is evolving quickly, you may want to cite also its version number (found with 'library(help = phangorn)').

Corresponding BibTeX entry:

  @Article{,
    title = {phangorn: phylogenetic analysis in R},
    author = {K.P. Schliep},
    journal = {Bioinformatics},
    year = {2011},
    volume = {27},
    number = {4},
    pages = {592--593},
  }