The source code is in https://github.com/beast-dev/tempest and is dependent on a library in https://github.com/beast-dev/beast-mcmc.
Rambaut A, Lam TT, Carvalho LM & Pybus OG (2016) Exploring the temporal structure of heterochronous sequences using TempEst. Virus Evolution 2: vew007 DOI: http://dx.doi.org/10.1093/ve/vew007