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Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
Boosting The Performance Of Bayesian Divergence Time Estimation With The Phylogenetic Likelihood Library, Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
Tracy Heath
We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineage-specific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Library (PLL), a fast, optimized, and parallelized collection of functions for conducting likelihood computations on phylogenetic trees. We show that, integrating the PLL into a likelihoodbased application is straight-forward since it took the first author (DD) a programming effort of only one month, without having prior knowledge of DPPDiv, nor the PLL. We achieve sequential speedups that range between a …