CONTML. Estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations. Does not assume a molecular clock. An alternative method of analyzing this data is to compute Nei's genetic distance and use one of the distance matrix programs. This program can also do maximum likelihood analysis of continuous characters that evolve by a Brownian Motion model, but it assumes that the characters evolve at equal rates and in an uncorrelated fashion, so that it does not take into account the usual correlations of characters.
CONTRAST. Reads a tree from a tree file, and a data set with continuous characters data, and produces the independent contrasts for those characters, for use in any multivariate statistics package. Will also produce covariances, regressions and correlations between characters for those contrasts. Can also correct for within-species sampling variation when individual phenotypes are available within a population.