A graphical method for detecting recombination in phylogenetic data sets
A graphical method for detecting recombination in phylogenetic data sets
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DOI：
10.1093/oxfordjournals.molbev.a025722
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发表时间：
1997-11-01
影响因子：
10.7
通讯作者：
Prentice, MJ
中科院分区：
文献类型：
--
作者：
McGuire, G;Wright, F;Prentice, MJ
目前的系统发育树重建方法假设沿着序列的所有位点存在单个潜在的树拓扑结构。由于重组而产生的镶嵌序列的存在违反了这一假设，并且由于在所有位点上强加单一的树形拓扑结构，将导致系统发育方法给出误导性的结果。因此，检测由重组引起的嵌合序列是系统发育分析中重要的第一步。一个图形化的方法检测重组，基于最小二乘法的系统发育估计，在这里。该方法通过沿着序列移动窗口来定位推定的重组断点。该方法的性能进行评估，通过模拟和其应用到一个真实的数据集。
Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for ail sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree topology on all sites. The detection of mosaic sequences caused by recombination is therefore an important first step in phylogenetic analysis. A graphical method for the detection of recombination, based on the least squares method of phylogenetic estimation, is presented here. This method locates putative recombination breakpoints by moving a window along the sequence. The performance of the method is assessed by simulation and by its application to a real data set.