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AliSim-HPC: parallel sequence simulator for phylogenetics.

Nhan Ly-Trong1, Giuseppe M J Barca1, Bui Quang Minh1

  • 1School of Computing, College of Engineering, Computing and Cybernetics, Australian National University, Canberra, ACT 2600, Australia.

Bioinformatics (Oxford, England)
|September 1, 2023
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Summary
This summary is machine-generated.

This study introduces AliSim-HPC, a new high-performance computing tool for faster phylogenetic sequence simulations. It significantly reduces simulation time for large datasets, enabling advanced phylogenetic research and machine learning applications.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Sequence simulation is crucial for evaluating phylogenetic methods, hypothesis testing, and machine learning in phylogenetics.
  • Existing simulators like AliSim are effective but slow for large datasets due to sequential implementation.
  • Parallelization has not been widely applied to sequence simulation, creating a bottleneck for large-scale data generation.

Purpose of the Study:

  • To develop a high-performance computing (HPC) version of the AliSim sequence simulator.
  • To significantly accelerate the simulation of large multiple sequence alignments for phylogenetic analyses.
  • To enable more efficient generation of training data for machine learning applications in phylogenetics.

Main Methods:

  • Introduced AliSim-HPC, a parallelized sequence simulation tool.
  • Employed multi-core parallelization using OpenMP for gap-free alignment simulations.
  • Utilized multi-CPU parallelization via Message Passing Interface (MPI) to support insertion-deletion models.

Main Results:

  • Achieved a 153-fold speedup in simulating 100 large gap-free alignments (30,000 sequences, 1 million sites).
  • Reduced simulation time from over one day to 11 minutes using 256 CPU cores.
  • The MPI version of AliSim-HPC supports complex insertion-deletion models, enhancing its applicability.

Conclusions:

  • AliSim-HPC offers a highly efficient and scalable solution for phylogenetic sequence simulations.
  • The tool dramatically reduces computational time, facilitating large-scale phylogenetic studies and ML applications.
  • AliSim-HPC is available as open-source software integrated with IQ-TREE v2.2.3.