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GPU MrBayes V3.1: MrBayes on Graphics Processing Units for Protein Sequence Data.

Shuai Pang1, Rebecca J Stones1, Ming-Ming Ren2

  • 1College of Computer and Control Engineering, Nankai University, Tianjin, China College of Software, Nankai University, Tianjin, China.

Molecular Biology and Evolution
|May 28, 2015
PubMed
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We developed GPU MrBayes V3.1 (ta(MC)(3)) for faster Bayesian phylogenetic inference on protein data. This enhanced tool processes larger datasets and improves accuracy and speed, outperforming existing software.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Bayesian phylogenetic inference is crucial for understanding evolutionary relationships.
  • Existing software like MrBayes can be computationally intensive, limiting analysis of large protein datasets.
  • Graphics Processing Units (GPUs) offer potential for accelerating complex computational tasks.

Purpose of the Study:

  • To present a modified GPU version of MrBayes, named ta(MC)(3) (GPU MrBayes V3.1).
  • To enhance the performance and capabilities of Bayesian phylogenetic inference software for protein data.

Main Methods:

  • Utilized 64-bit variables to enable processing of larger datasets.
  • Implemented Kahan summation to improve computational accuracy and convergence rates.
Keywords:
GPUMrBayesphylogeneticsprotein

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  • Leveraged GPU acceleration for significant runtime improvements.

    • Main Results:

    • Achieved speedups of up to 2.5x compared to the fastest current software.
    • Demonstrated speedups of up to 90x compared to serial MrBayes.
    • Observed further performance gains on multi-GPU hardware.

    Conclusions:

    • GPU MrBayes V3.1 (ta(MC)(3)) offers a substantial performance improvement for Bayesian phylogenetic inference.
    • The enhanced software enables analysis of larger protein datasets with improved accuracy and speed.
    • This tool is publicly available for the scientific community.