Benchmarking BEAGLE to find optimal parameters for BEAST X

Abstract

Bayesian phylogenetic analyses are notoriously time-consuming, largely because exploring the posterior distribution requires computing Felsensteins likelihood. The BEAGLE library is a high-performance computational tool that dramatically accelerates the calculation of such likelihoods by leveraging parallel processing on GPUs, multicore CPUs, and SSE vectorisation. Here we present results from benchmarking a widely popular phylogenetics package, BEAST X, using BEAGLE integration, focusing on how hardware allocation affects running times. We demonstrate substantial differences among BEAGLE settings on real Dengue Virus (DENV) data, both with and without partitioning. Using simulated sequences, we establish guidelines for GPU usage in BEAST X runs. These guidelines can be used for effective resource allocation for empirical analyses and simulation studies.