Automated phylogenetic detection of recombination using a genetic algorithm
Automated phylogenetic detection of recombination using a genetic algorithm
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DOI：
10.1093/molbev/msl051
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发表时间：
2006-10-01
影响因子：
10.7
通讯作者：
Frost, Simon D. W.
中科院分区：
文献类型：
--
作者：
Kosakovsky Pond, Sergei L.;Posada, David;Frost, Simon D. W.
受重组或基因转换影响的同源序列的进化不能用单一的系统发育树来充分解释。许多基于树的序列分析方法，例如用于检测非中性进化位点的方法，如果忽略这种系统发育的不一致性，已被证明会失败。然而，有可能提出几种可以正确模拟非重组片段进化的系统发育学。我们提出了一个基于模型的框架，该框架使用遗传算法来搜索多序列比对以寻找假定的重组断点，量化对其位置的支持水平，并识别涉及假定重组事件的序列或进化枝。软件实现可以在分布式计算环境中快速有效地运行，并且可以选择方法的各种组件以实现计算便利性或统计严谨性。我们评估了新方法在模拟比对和一系列已发布的基准数据集上的性能。最后，我们证明用我们的方法进行预筛选比对可以分析重组序列以进行正选择。
The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.