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README.md

README.md

DPPDiv

DPPDiv is a program for estimating divergence times on a fixed, rooted tree topology

Details about this program are available in the following papers:

*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)

The DPPDiv users discussion group: https://groups.google.com/forum/#!forum/dppdiv-users

This version of DPPDiv includes a new fossil calibration model called the 'fossilized birth-death' (FBD) process. (Work by Tracy Heath, John Huelsenbeck, and Tanja Stadler)

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