Phylogenetics: just methods

The number of available methods in phylogeny and systematics may appear to be daunting not only to beginning students but also to well-established researchers. Admittedly, anyone with a copy of, say, PAUP* can learn how to "point and shoot" to make a neighbor-joining tree, or a cladogram or a likelihood tree, but this doesn't really mean you know what you're doing and we suspect that you'd probably like to know. This site is designed to do that. To provide you with an understanding of the various methods you might encounter so as to allow you to make informed decisions about what you think is defensible and appropriate.


  1. Unweighted Pair Group Method
    (UPGMA, phenetics)
    Weighted Pair Group Method
    (WPGMA, phenetics)

  2. Hennigian Argumentation (cladistics)
    Constructing Wagner Trees (cladistics)

  3. Tree Think - important terminology regarding trees, homomplasy, apomorphies, etc.

  4. Parsimony Analysis -
    optimization, tree searching (cladistics)

  5. weighting

  6. Distance Analyses including 'minimum evolution', Neighbor Joining and models of stochastic DNA change

  7. Much more on models of change

  8. Maximum Likelihood

  9. Differences of opinion between parsimony and likelihood

  10. Multiple Sequence Alignment

  11. Optimization Alignment (POY)

    Contact: Mark E. Siddall ph: 212 769 5638

    This site updated April 2007