dppdiv's Introduction

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)

*Warnock, Heath, Stadler. 2020. Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates. Paleobiology, DOI: 10.1017/pab.2020.12

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)

This version can also be used to estimate speciation, extinction and fossil recovery rates from stratigraphic range data under the constant rate FBD range process. (Work by Rachel Warnock, Tracy Heath, and Tanja Stadler)

dppdiv's People