BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
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 an...
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| Vydáno v: | Systematic biology Ročník 61; číslo 1; s. 170 - 173 |
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| Hlavní autoři: | , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
England
Oxford University Press
01.01.2012
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| Témata: | |
| ISSN: | 1063-5157, 1076-836X, 1076-836X |
| On-line přístup: | Získat plný text |
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| Abstract | 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. |
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| AbstractList | 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.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. 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. 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. |
| Author | Beerli, Peter Swofford, David L. Huelsenbeck, John P. Suchard, Marc A. Zwickl, Derrick J. Cummings, Michael P. Darling, Aaron Lewis, Paul O. Rambaut, Andrew Ronquist, Fredrik Holder, Mark T. Ayres, Daniel L. |
| Author_xml | – sequence: 1 givenname: Daniel L. surname: Ayres fullname: Ayres, Daniel L. email: ayres@umiacs.umd.edu organization: 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA – sequence: 2 givenname: Aaron surname: Darling fullname: Darling, Aaron email: a.rambaut@ed.ac.uk organization: 2Genome Center, University of California, Davis, CA 95616, USA – sequence: 3 givenname: Derrick J. surname: Zwickl fullname: Zwickl, Derrick J. email: a.rambaut@ed.ac.uk organization: 3Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA – sequence: 4 givenname: Peter surname: Beerli fullname: Beerli, Peter email: a.rambaut@ed.ac.uk organization: 4Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA – sequence: 5 givenname: Mark T. surname: Holder fullname: Holder, Mark T. email: a.rambaut@ed.ac.uk organization: 3Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA – sequence: 6 givenname: Paul O. surname: Lewis fullname: Lewis, Paul O. email: a.rambaut@ed.ac.uk organization: 5Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA – sequence: 7 givenname: John P. surname: Huelsenbeck fullname: Huelsenbeck, John P. email: a.rambaut@ed.ac.uk organization: 6Department of Integrative Biology, University of California, Berkeley, CA 94720, USA – sequence: 8 givenname: Fredrik surname: Ronquist fullname: Ronquist, Fredrik email: a.rambaut@ed.ac.uk organization: 7Swedish Museum of Natural History, 114 18 Stockholm, Sweden – sequence: 9 givenname: David L. surname: Swofford fullname: Swofford, David L. email: a.rambaut@ed.ac.uk organization: 8Center for Evolutionary Genomics, Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA – sequence: 10 givenname: Michael P. surname: Cummings fullname: Cummings, Michael P. email: a.rambaut@ed.ac.uk organization: 1Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA – sequence: 11 givenname: Andrew surname: Rambaut fullname: Rambaut, Andrew email: a.rambaut@ed.ac.uk organization: 9Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK; E-mail: a.rambaut@ed.ac.uk – sequence: 12 givenname: Marc A. surname: Suchard fullname: Suchard, Marc A. email: a.rambaut@ed.ac.uk organization: 11Department of Biomathematics |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/21963610$$D View this record in MEDLINE/PubMed |
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| Keywords | Bayesian phylogenetics GPU parallel computing maximum likelihood |
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| References | 19369496 - Bioinformatics. 2009 Jun 1;25(11):1370-6 12912839 - Bioinformatics. 2003 Aug 12;19(12):1572-4 17996036 - BMC Evol Biol. 2007;7:214 20147900 - Nature. 2010 Feb 25;463(7284):1079-83 7288891 - J Mol Evol. 1981;17(6):368-76 |
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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... 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... |
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| Title | BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics |
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