ExaML版本3：一种用于超级计算机上系统发育基因组分析的工具。
ExaML version 3: a tool for phylogenomic analyses on supercomputers.
作者信息
Kozlov Alexey M, Aberer Andre J, Stamatakis Alexandros
机构信息
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and.
Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany and Department of informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
出版信息
Bioinformatics. 2015 Aug 1;31(15):2577-9. doi: 10.1093/bioinformatics/btv184. Epub 2015 Mar 29.
Abstract
MOTIVATION
Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers.
RESULTS
We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms.
摘要
动机
系统发育树在医学和生物学研究的各个领域中使用得越来越频繁。由于新一代测序技术的变革，用于进行系统发育分析的数据集以前所未有的速度增长。我们展示了ExaML版本3，这是一个专门用于在超级计算机上对全转录组和全基因组比对进行系统发育树推断的生产级代码。
结果
我们对ExaML进行了多项改进和扩展：替换模型和支持的数据类型的扩展、一种新型负载平衡算法的集成以及显著提高并行效率的并行I/O优化，以及基于英特尔MIC硬件平台的生产级实现。
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