The field of phylogenetic comparative methods is a very young field of evolutionary biology which attempts to account for phylogenetic correlations among comparative trait data. Many PCM methods have been and are being developed in this field, creating a rapidly expanding base of analyses from which to choose. A key aspect to consider in any PCM-based study is phylogenetic signal, the statistical measure of the phylogenetic clumping of similarities in the evolution of traits. Here are some links that are relevant to anyone interested in computational PCM and its recent advances.
Ted Garland, Jr.
http://www.biology.ucr.edu/people/faculty/Garland/Garland2.html
http://www.biology.ucr.edu/people/faculty/Garland/PDAP.html
Simon Blomberg
http://profiles.bacs.uq.edu.au/Simon.Blomberg.html
Perhaps the latest PCM application for evaluating phylogenetic signal
adephylo