The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
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DOI：
10.1109/tcbb.2009.68
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发表时间：
2011-07-01
影响因子：
4.5
通讯作者：
Warnow, Tandy
中科院分区：
文献类型：
--
作者：
Wang, Li-San;Leebens-Mack, Jim;Warnow, Tandy
多序列比对通常是估计系统发育树的第一步，假设随着比对的改善，系统发育重建也会改善。在过去的十年左右，新的多序列比对方法已经开发出来，以改善蛋白质结构的比较分析，但这些新方法还没有典型地用于系统发育分析。在本文中，我们报告了一个模拟研究，我们进行了评估的后果，使用这些新的多序列比对方法在所得到的系统发育重建。我们发现，虽然对齐准确性与系统发育准确性呈正相关，但从改进的对齐中得到的系统发育估计的改善量可以从很小到很大。我们观察到，系统发育的准确性是最高度相关的比对准确性时，序列是最难对齐，而在比对准确性的变化可以有系统发育的准确性时，比对错误率一般较低的影响很小。我们讨论这些意见和影响，为今后的工作。
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.