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MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Thomas M Keane1, Thomas J Naughton, James O McInerney

  • 1Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Hinxton, UK. tkeane@cs.nuim.ie

Nucleic Acids Research
|June 8, 2007
PubMed
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This study introduces MultiPhyl, a distributed computing platform for large-scale phylogenetics. It harnesses idle computers to accelerate evolutionary history analysis for numerous gene families.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • The increasing number of sequenced genomes fuels demand for large-scale phylogenomic analyses.
  • Maximum Likelihood (ML) is a highly accurate phylogenetic construction method.
  • Current ML methods face computational limitations for analyzing numerous gene families on single machines.

Purpose of the Study:

  • To present MultiPhyl, the first high-throughput distributed phylogenetics platform.
  • To enable the analysis of evolutionary history for many gene families by leveraging distributed computing.
  • To provide a scalable solution for computationally intensive phylogenetic tasks.

Main Methods:

  • Developed MultiPhyl, a distributed computing platform utilizing heterogeneous, non-dedicated machines.

Related Experiment Videos

  • Implemented a phylogenetics supercomputer by aggregating idle computational resources.
  • Integrated model selection, tree searching, and bootstrapping for numerous gene family alignments.

    • Main Results:

    • MultiPhyl successfully enables high-throughput phylogenomic analysis.
    • The platform utilizes a wide array of 88 amino acid and 56 nucleotide ML models.
    • It supports simultaneous analysis of thousands of gene family alignments.

    Conclusions:

    • MultiPhyl significantly accelerates phylogenomic analyses by utilizing distributed computing.
    • The platform offers a practical solution for researchers analyzing large datasets.
    • A public webserver is available for MultiPhyl at http://www.cs.nuim.ie/distributed/multiphyl.php.