BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

By Daniel L. Ayres, Aaron E. Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings and 2 more. Systematic Biology, 2011

656 citations recorded by the source corpus.

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/3ed73bc1555bcd07051c234dce710f9eb540034a

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Citations in the corpus

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018, methodology): “To improve efficiency for large-scale sequence data, BEAST 1.10 uses the BEAGLE library (Ayres et al. 2012) that provides access to massive parallelization on a range of computing architectures.”
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space (2012, methodology): “Importantly, MrBayes 3.2 also supports the use of the BEAGLE library for likelihood calculations (Ayres et al. 2012).”
Bayesian Phylogenetics with BEAUti and the BEAST 1.7 (2012, methodology): “7 integrates with and provides a GUI interface to configure the BEAGLE library (Ayres et al. 2011) that utilizes multicore processors, vectorization, and massively parallel graphics processors to substantially decrease BEAST runtimes (Suchard and Rambaut 2009).”
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis (2014, methodology): “BEAST2 implements a range of techniques to improve sampling performance including multi-core parallelization, vector and GPU approaches to fine scale parallelization through the use of the BEAGLE library [10,11].”
Modeling infectious disease dynamics in the complex landscape of global health (2015, neutral): “Similarly, although progress has been made in scaling inference from genes to genomes (33), scaling inference to large numbers of sequences is lagging far behind.”