An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data
An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data
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用于计算 DNA 数据系统发育似然函数的优化可重构系统
DOI：
10.1109/ipdpsw.2012.43
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发表时间：
2012
期刊：
影响因子：
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通讯作者：
A. Stamatakis
中科院分区：
文献类型：
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作者：
S. Berger;Nikolaos S. Alachiotis;A. Stamatakis
系统发育似然函数(PLF)是评价系统发育树的重要统计函数。为此，PLF是所有最先进的基于可能性的系统发育推理程序的计算核心。通常，它占这类程序总执行时间的85%以上。基于以往在可重构逻辑上实现PLF的经验，我们提出了一种用于计算PLF的显著改进的硬件结构。我们的新设计针对计算四状态(DNA)输入数据的PLF进行了优化。它还适应于现实世界树推理程序的计算要求，完全独立于手头的特定树搜索算法。此外，我们还描述了如何修改和适应我们的体系结构，以处理一般的n状态数据，如蛋白质(20个状态)或RNA二级结构数据(6、7或16个状态，具体取决于模型)。最后，我们设计了一个接口机制，使得我们的PLF硬件体系结构可以与广泛使用的系统发育推理工具RAxML进行交互。我们采用了现场可编程门阵列技术来验证该架构的正确性，并对其进行性能评估。
The Phylogenetic Likelihood Function (PLF) is an important statistical function for evaluating phylogenetic trees. To this end, the PLF is the computational kernel of all state-of-the-art likelihood-based phylogenetic inference programs. Typically, it accounts for more than 85% of total execution time in such programs. We present a substantially improved hardware architecture for computing the PLF based on previous experiences with implementing the PLF on reconfigurable logic. Our new design is optimized for computing the PLF on four-state (DNA) input data. It is also adapted to the computational requirements of real-world tree inference programs and completely independent of the specific tree search algorithm at hand. Furthermore, we describe how our architecture can be modified and adapted to handle general n-state data, such as protein (20 states) or RNA secondary structure data (6, 7, or 16 states, depending on the model). Finally, we designed an interface mechanism such that our PLF hardware architecture can interact with the widely-used phylogenetic inference tool RAxML. We deploy FPGA technology to verify the correctness of the architecture and to evaluate performance.