DPPDiv is a program for estimating species divergence times and lineage-specific substitution rates on a fixed topology. The prior on branch rates is a Dirichlet process prior which clusters branches into distinct rate classes. Alternative priors including the global molecular clock and the independent rates model are also available. The priors on node ages include the birth-death (and Yule) model and the uniform distribution.
A fast/optimized version of DPPDiv (modified by Tomáš Flouri and Alexandros Stamatakis) is available here (recommended version): FastDPPDiv
An extended version of FastDPPDiv with a coherent model for fossil calibration is available on GitHub: FDPPDIV
The original source code can be downloaded here: DPPDiv
DPPDiv user discussion email list: https://groups.google.com/d/forum/dppdiv-users
Descriptions of models and implementation
- Heath, Huelsenbeck, Stadler. 2013. The fossilized birth-death process: A coherent model of fossil calibration for divergence time estimation. arXiv preprint arXiv:1310.2968.
- Heath, Holder, Huelsenbeck. 2012. A Dirichlet process prior for estimating lineage-specific substitution rates. Molecular Biology and Evolution 29:939-955.
- Heath. 2012. A hierarchical Bayesian model for calibrating estimates of species divergence times. Systematic Biology, 61:793-809.
- Flouri, Stamatakis. 2012. An Improvement to DPPDIV. Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-7. (Technical report on optimization and parallelization of DPPDiv)
- Darriba, Aberer, Flouri, Heath, Izquierdo-Carrasco, Stamatakis: "Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library", accepted for publication at IPDPS 2013, Boston, USA, 2013. (peer-reviewed conference paper) [pdf]