To cite medusa, auteur, MECCA, or geiger in a publication use:

medusa

  Alfaro, M. E., F. Santini, C. Brock, H. Alamillo, A. Dornburg, D. L.
  Rabosky, G. Carnevale, and L. J. Harmon (2009) Nine exceptional
  radiations plus high turnover explain species diversity in jawed
  vertebrates. PNAS, 106, 13410-13414.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates},
    author = {M. E. Alfaro and F. Santini and C. Brock and H. Alamillo and A. Dornburg and D. L. Rabosky and G. Carnevale and L. J. Harmon},
    journal = {PNAS},
    year = {2009},
    volume = {106},
    pages = {13410-13414},
    doi = {10.1073/pnas.0811087106},
  }

auteur

  Eastman, J. M, M. E. Alfaro, P. Joyce, A. L. Hipp, and L. J. Harmon
  (2011) A novel comparative method for identifying shifts in the rate
  of character evolution on trees. Evolution, 65, 3578-3589.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {A novel comparative method for identifying shifts in the rate of character evolution on trees},
    author = {J. M. Eastman and M. E Alfaro and P. Joyce and A. L. Hipp and L. J. Harmon},
    journal = {Evolution},
    year = {2011},
    volume = {65},
    pages = {3578-3589},
    doi = {10.1111/j.1558-5646.2011.01401.x},
  }

MECCA

  Slater, G. J., L. J. Harmon, D. Wegmann, P. Joyce, L. J. Revell, and
  M. E. Alfaro (2012) Fitting models of continuous trait evolution to
  incompletely sampled comparative data using approximate Bayesian
  computation. Evolution, 66, 752-762.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation},
    author = {G. J. Slater and L. J. Harmon and D. Wegmann and P Joyce and L. J. Revell and M. E. Alfaro},
    journal = {Evolution},
    year = {2012},
    volume = {66},
    pages = {752-762},
    doi = {10.1111/j.1558-5646.2011.01474.x},
  }

geiger-orig

  Harmon, L. J., J. T. Weir, C. D. Brock, R. E. Glor, and W. Challenger
  (2008) GEIGER: investigating evolutionary radiations. Bioinformatics,
  24, 129-131.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {GEIGER: investigating evolutionary radiations},
    author = {L. J. Harmon and J. T. Weir and C. D. Brock and R. E. Glor and W. Challenger},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    pages = {129-131},
    doi = {10.1093/bioinformatics/btm538},
  }

geiger

  Pennell, M. W., J. M. Eastman, G. J. Slater, J. W. Brown, J. C.
  Uyeda, R. G. FitzJohn, M. E. Alfaro, and L. J. Harmon {2014} geiger
  v2.0: an expanded suite of methods for fitting macroevolutionary
  models to phylogenetic trees. Bioinformatics, 30, 2216-2218.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees},
    author = {M. W. Pennell and J. M. Eastman and G. J. Slater and J. W. Brown and J. C. Uyeda and R. G. Fitzjohn and M. E. Alfaro and L. J. Harmon},
    journal = {Bioinformatics},
    year = {2014},
    volume = {30},
    pages = {2216-2218},
    doi = {10.1093/bioinformatics/btu181},
  }