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

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 realist... Full description

Journal Title: Systematic biology 2012-01-01, Vol.61 (1), p.170-173
Main Author: Ayres, Daniel L
Other Authors: Darling, Aaron , Zwickl, Derrick J , Beerli, Peter , Holder, Mark T , Lewis, Paul O , Huelsenbeck, John P , Ronquist, Fredrik , Swofford, David L , Cummings, Michael P , Rambaut, Andrew , Suchard, Marc A
Format: Electronic Article Electronic Article
Language: English
Subjects:
GPU
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/21963610
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recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3243739
title: BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
format: Article
creator:
  • Ayres, Daniel L
  • Darling, Aaron
  • Zwickl, Derrick J
  • Beerli, Peter
  • Holder, Mark T
  • Lewis, Paul O
  • Huelsenbeck, John P
  • Ronquist, Fredrik
  • Swofford, David L
  • Cummings, Michael P
  • Rambaut, Andrew
  • Suchard, Marc A
subjects:
  • Algorithms
  • Application programming interfaces
  • Bayesian phylogenetics
  • Bioinformatics
  • Biological evolution
  • Codons
  • Computational Biology - methods
  • Computer software
  • Computing Methodologies
  • Datasets
  • Evolution
  • Evolution, Molecular
  • Genome
  • GPU
  • Inference
  • Libraries
  • maximum likelihood
  • parallel computing
  • Phylogenetics
  • Phylogeny
  • Software
  • Software for Systematics
  • SOFTWARE FOR SYSTEMATICS AND EVOLUTION
ispartof: Systematic biology, 2012-01-01, Vol.61 (1), p.170-173
description: 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.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionPhylogenetic 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.
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subjectAlgorithms ; Application programming interfaces ; Bayesian phylogenetics ; Bioinformatics ; Biological evolution ; Codons ; Computational Biology - methods ; Computer software ; Computing Methodologies ; Datasets ; Evolution ; Evolution, Molecular ; Genome ; GPU ; Inference ; Libraries ; maximum likelihood ; parallel computing ; Phylogenetics ; Phylogeny ; Software ; Software for Systematics ; SOFTWARE FOR SYSTEMATICS AND EVOLUTION
ispartofSystematic biology, 2012-01-01, Vol.61 (1), p.170-173
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descriptionPhylogenetic 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.
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titleBEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
authorAyres, Daniel L ; Darling, Aaron ; Zwickl, Derrick J ; Beerli, Peter ; Holder, Mark T ; Lewis, Paul O ; Huelsenbeck, John P ; Ronquist, Fredrik ; Swofford, David L ; Cummings, Michael P ; Rambaut, Andrew ; Suchard, Marc A
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abstractPhylogenetic 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.
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