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High performance phylogenetic analysis on CUDA-compatible GPUs

Published:25 March 2012Publication History
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Abstract

The operation of phylogenetic analysis aims to investigate the evolution and relationships among species. It is widely used in the fields of system biology and comparative genomics. However, phylogenetic analysis is also a computationally intensive operation as the number of tree topology grows in a factorial way with the number of species involved. Therefore, due to the large number of species in the real world, the computational burden has largely thwarted phylogenetic reconstruction. In this paper, we describe the detailed GPU-based multi-threaded design and implementation of a Markov Chain Monte Carlo (MCMC) maximum likelihood algorithm for phylogenetic analysis on a set of aligned nucleotide sequences. The implementation is based on the framework of the most widely used phylogenetic analysis tool, namely MrBayes. The proposed approach resulted in 6x-8x speed-up on an NVidia Geforce 460 GTX GPU compared to an optimized GPP-based software implementation running on a desktop computer with a single Intel Xeon 2.53 GHz CPU and 6.0 GB RAM.

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      • Published in

        cover image ACM SIGARCH Computer Architecture News
        ACM SIGARCH Computer Architecture News  Volume 40, Issue 5
        ACM SIGARCH Computer Architecture News/HEART '12
        December 2012
        110 pages
        ISSN:0163-5964
        DOI:10.1145/2460216
        Issue’s Table of Contents

        Copyright © 2012 Authors

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        Association for Computing Machinery

        New York, NY, United States

        Publication History

        • Published: 25 March 2012

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