GARD: a genetic algorithm for recombination detection
GARD: a genetic algorithm for recombination detection
复制标题
DOI：
10.1093/bioinformatics/btl474
复制
发表时间：
2006-12-15
期刊：
影响因子：
5.8
通讯作者：
Frost, Simon D. W.
中科院分区：
文献类型：
--
作者：
Pond, Sergei L. Kosakovsky;Posada, David;Frost, Simon D. W.
动机：如果不考虑重组，系统发育和进化推断可能会被严重误导，因此，筛选重组应该是几乎每一项比较研究的重要组成部分。重组序列的进化不能用单一的系统发育树来正确解释，但可以用几个系统发育树来正确地模拟非重组片段的进化。结果：我们开发了一种基于似然性的模型选择程序，该程序使用遗传算法来搜索多个序列比对以寻找重组断裂点的证据，并识别假定的重组序列。GARD是一种可扩展且直观的方法，可以高效地并行运行。广泛的模拟研究表明，该方法在能力和准确性方面几乎总是优于其他可用的工具，而且使用GARD来筛选重组序列确保了旨在检测肯定选择的方法具有良好的统计特性。可用性：免费提供http://www.datamonkey.org/GARD/Contact：Spond@ucsd.edu
Motivation: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.Results: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.Availability: Freely available http://www.datamonkey.org/GARD/Contact: spond@ucsd.edu