TempEst (formerly known as ‘Path-O-Gen’) is a tool for investigating the temporal signal and ‘clocklikeness’ of molecular phylogenies. It can read and analyse contemporaneous trees (where all sequences have been collected at the same time) and dated-tip trees (where sequences have been collected at different dates). It is designed for analysing trees that have not been inferred under a molecular-clock assumption to see how valid this assumption may be. It can also root the tree at the position that is likely to be the most compatible with the assumption of the molecular clock.
You can download TempEst from here: http://tree.bio.ed.ac.uk/software/tempest/
A. Rambaut, T. T. Lam, L. M. Carvalho and O. G. Pybus (2016) Exploring the temporal structure of heterochronous sequences using TempEst. Virus Evolution 2(1): vew007. DOI: http://dx.doi.org/10.1093/ve/vew007