CuPhylo: A CUDA Based Application Program Interface and Library for Phylogenetic Analysis

Phylogenetics is the study of evolutionary history and relationships among individuals. Phylogenetic analysis plays an important role in understanding biodiversity, evolution, ecology and genome. Nowadays, the two major phylogenetic analysis approaches are Maximum Likelihood method and Bayesian method, and their most time-consuming parts are all the likelihood computations. In this paper, we present a CUDA based computing Application Program Interface (API) and library called CuPhylo for the likelihood computation in phylogenetic analysis. Experimental results indicate that CuPhylo outperforms another phylogenetic likelihood computation library BEAGLE on large-scale data sets. For instance, if state number is 61 (codon model), CuPhylo achieves a highest 3.86 times speedup when compared to BEAGLE. CuPhylo is available from https://github.com/rmingming/CuPhylo.