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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE.

Guy Baele¹, Daniel L Ayres², Andrew Rambaut³

¹Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium. guy.baele@kuleuven.be.

Methods in Molecular Biology (Clifton, N.J.)

|July 7, 2019

Summary

This summary is machine-generated.

The Broad-Platform Evolutionary Analysis General Likelihood Evaluator (BEAGLE) library significantly speeds up computational time for phylogenomic and phylodynamic analyses. Utilizing graphics processing units (GPUs) with BEAGLE offers substantial advancements for large molecular datasets.

Keywords:

Adaptive Markov chain Monte Carlo BEAGLE BEAST Bayesian phylogenetics Data integration Generalized linear model High-performance computing Multipartite data Pathogen phylodynamics Phylogenomics

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Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Statistical phylogenomics and phylodynamics involve significant computational challenges.
High-performance computing is crucial for analyzing large molecular sequence datasets.

Purpose of the Study:

To evaluate the computational benefits of the BEAGLE library in phylogenomic and phylodynamic analyses.
To compare the performance of CPUs and GPUs for likelihood computations using BEAGLE.

Main Methods:

Utilized the BEAGLE high-performance library for likelihood computations.
Compared computational performance between multicore CPUs and various GPUs.
Benchmarked performance using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software.
Focused on evolutionary models and datasets of varying dimensions.

Main Results:

BEAGLE substantially reduces computation time in phylogenomic and phylodynamic analyses.
GPUs demonstrate significant computational advantages over CPUs for large datasets when using BEAGLE.
Performance improvements were observed across various evolutionary models and hardware configurations.

Conclusions:

The BEAGLE library provides substantial computational advancements for phylogenomic and phylodynamic analyses.
GPUs, when utilized with BEAGLE, offer tremendous computational power for large molecular sequence data.
BEAGLE is a valuable tool for both Bayesian inference and maximum-likelihood frameworks in evolutionary analyses.