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Presentation
Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library
2013 IEEE 27th International Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW) (2013)
  • Diego Darriba, University of Vigo
  • Andre Aberer, Heidelberg Institute for Theoretical Studies
  • Tomas Flouri, Heidelberg Institute for Theoretical Studies
  • Tracy A. Heath, University of California, Berkeley
  • Fernando Izquierdo-Carrasco, Heidelberg Institute for Theoretical Studies
  • Alexandros Stamatakis, Heidelberg Institute for Theoretical Studies
Abstract
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 factor of two to three and near-optimal parallel speedups up to 48 threads on sufficiently large datasets. Hence, with a programming effort of one month, we were able to improve DPPDiv's time-to-solution on parallel systems by two orders of magnitude and also to substantially improve its ability to infer divergence times on large-scale datasets.
Keywords
  • Phylogenetics,
  • Parallel computing,
  • Divergence time estimation,
  • Programming effort,
  • Phylogenetic likelihood
Publication Date
May, 2013
Location
Boston, MA
DOI
10.1109/IPDPSW.2013.267
Citation Information
Darriba, Aberer, Flouri, Heath, Izquierdo-Carrasco, Stamatakis. 2013. Boosting the performance of Bayesian divergence time estimation with the Phylogenetic Likelihood Library. Parallel and Distributed Processing Symposium Workshops PhD Forum (IPDPSW), 2013 IEEE 27th International, Boston, USA, pp. 539-548.