Enabling Research in Evolutionary Biology
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 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.
For more details about PLL-DPPDIV read the paper.
To obtain PLL-DPPDIV visit the official GitHub repository.
Download the open source code of the optimized (using vector intrinsics) and parallelized version (using OpenMP) of the DPPDIV (original code by Tracy Heath) code for estimating divergence times with a dirichilet process prior here.
For details about the program please read the paper.
When using the optimized DPPDIV code please cite the original paper:
T. A. Heath, M.T. Holder, J.P. Huelsenbeck: "A Dirichlet process prior for estimating lineage-specific substitution rates". Molecular Biology and Evolution, 2011.
and the technical report below:
T. Flouri, A. Stamatakis: "An Improvement to DPPDIV", Heidelberg Institute for Theoretical Studies, Exelixis-RRDR-2012-7, August 2012. PDF
For support please use the DPPDIV google group.