Maximum-Likelihood Methods for Phylogeny Estimation

Maximum-likelihood (ML) estimation of phylogenies has reached a rather high level of sophistication because of algorithmic advances, improvements in models of sequence evolution, and improvements in statistical approaches and application of cluster computing. Here, I provide a brief basic background in application of the general principle of ML estimation to phylogenetics and provide an example of selecting among a nested set of ML models using a dynamic approach to hierarchical likelihood-ratio tests. I focus attention on PAUP∗ because it provides unique ease of switching among alternative optimality criteria (e.g., minimum evolution, parsimony, and ML). Further, examples of parametric bootstrap tests are provided that demonstrate statistical tests of phylogenetic hypotheses and model adequacy, in an absolute rather than relative sense. The increasing availability of clustered, parallelized computation makes use of such parametric approaches feasible.