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DPPDiv on XSEDE

DPPDiv is a program by Tracy Heath 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.

The CIPRES Science Gateway provides the fast/optimized version of DPPDiv (as modified by Tomáš Flouri and Alexandros Stamatakis).

Manual for DPPDIV: We are unaware of the existence of a manual for DPPDiv.

DPPDiv Google Group: https://groups.google.com/forum/#!forum/dppdiv-users

DPPDiv home page: none known.

References:

• 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)

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