JH advocates that you use tree stochastic variation as null hypothesis. Standard likelihood ratio test that can be used. Assimilate data under null hypothesis and then test. It takes more time to analyze a data set, but you may not need as many taxa because of the flexibility. If have branch length heterogeneity can have long branch attraction which is a violation of assumptions of model.
Parsimony is a fairly restrictive model.
DL working at GenBank and organizing data in a meaningful taxonomic way. Organisms at GenBank as of Dec 15, 1995. Currently 18000 organisms including all types of sequences. Currently fungi are most active. For every organism at GenBank there is generally only one sequence.