BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
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DOI：
10.1093/sysbio/syr100
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发表时间：
2012-01
影响因子：
6.5
通讯作者：
Suchard MA
中科院分区：
文献类型：
--
作者：
Ayres DL;Darling A;Zwickl DJ;Beerli P;Holder MT;Lewis PO;Huelsenbeck JP;Ronquist F;Swofford DL;Cummings MP;Rambaut A;Suchard MA
系统发育推断是我们理解生命起源和进化的基础，近年来，人们对贝叶斯推理和最大似然估计等统计方法产生了浓厚的兴趣。然而，对于大数据集和现实或有趣的进化模型，这些方法仍然需要计算。高通量测序可以产生数千个分类群的数据，但使用序列计算来解决此类问题通常需要使用非统计或近似方法。最近图形处理单元(GPU)的出现为利用其出色的浮点计算性能来加速统计系统发育推断提供了机会。一个专门的系统发育计算库将使现有的软件包能够更有效地利用现有的计算机硬件，包括图形处理器。采用共用库也将使其他新兴的计算体系结构，如现场可编程门阵列，在未来更容易使用。我们介绍了Beagle，一个用于高性能统计系统发育推理的应用程序编程接口(API)和库。该API提供了用于在各种计算硬件平台上执行系统发生可能性计算的统一接口。该库包括一组高效的实现，目前可以利用硬件，包括使用NVIDIA CUDA的GPU、具有SIMD流扩展和相关处理器补充指令集的中央处理单元(CPU)，以及通过OpenMP的多核CPU。为了证明通用API的优势，我们将该文库整合到几个流行的系统发育软件包中。Beagle库是免费开放源码软件，许可使用较宽松的通用公共许可证，可从http://beagle-lib.googlecode.com.获得示例客户端程序可以作为公共域软件获得。
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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影响因子：
64.8
作者：
Regier, Jerome C.;Shultz, Jeffrey W.;Cunningham, Clifford W.
通讯作者：
Cunningham, Clifford W.
影响因子：
5.8
作者：
Suchard, Marc A.;Rambaut, Andrew
通讯作者：
Rambaut, Andrew
影响因子：
3.9
作者：
FELSENSTEIN, J
通讯作者：
FELSENSTEIN, J
影响因子：
5.8
作者：
Ronquist, F;Huelsenbeck, JP
通讯作者：
Huelsenbeck, JP