title: GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data.
abstract: We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC)(3) (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC)(3) to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/.
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Pang
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: Stones
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China renmingming@nbjl.nankai.edu.cn.
authors.forename: Ming-Ming
authors.initials: MM
authors.lastname: Ren
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.
authors.forename: Xiao-Guang
authors.initials: XG
authors.lastname: Liu
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Wang
authors.affiliation: College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.
authors.forename: Hong-ju
authors.initials: HJ
authors.lastname: Xia
authors.affiliation: College of Life Science, Nankai University, Tianjin, China.
authors.forename: Hao-Yang
authors.initials: HY
authors.lastname: Wu
authors.affiliation: College of Life Science, Nankai University, Tianjin, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: College of Life Science, Nankai University, Tianjin, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Xie
mesh_terms: D001499:Bayes Theorem; D019295:Computational Biology; D003196:Computer Graphics; D010802:Phylogeny; D020539:Sequence Analysis, Protein; D012984:Software
keywords: GPU; MrBayes; phylogenetics; protein