AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support.
AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support.
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Aligroove - 在多个序列比对中异质序列差异的访问和膨胀的分支支持的检测。
DOI：
10.1186/1471-2105-15-294
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发表时间：
2014-08-30
影响因子：
3
通讯作者：
Misof B
中科院分区：
文献类型：
--
作者：
Kück P;Meid SA;Groß C;Wägele JW;Misof B
掩蔽多个序列比对块已成为增强底层数据树状相似性的一种强有力的方法。然而，现有的掩蔽方法对异质序列差异不敏感，这可能会误导树重建。提出了一种基于滑动窗口和蒙特卡罗重采样方法的新方法AliGROOVE，该方法可视化了多序列比对中与单个类群或类群子集相关的异质序列分歧或比对歧义，并标记了给定树上的可疑分支。我们使用模拟的多序列比对来表明，两两序列比对中的比对歧义程度与树重建中的错位分类群的频率相关。在AliGROOVE中实现的方法允许检测树中支持的节点，尽管在潜在的多序列比对中缺乏系统发育信号。在一个基于海龟线粒体DNA序列的经验数据集的案例研究中，我们证明了AliGROOVE同样能够很好地检测到异质序列差异。AliGROOVE方法有可能识别与多序列比对中的其他分类群相比主要表现出随机序列相似性的单个分类群或分类群的亚集。它还允许以一种新的方式来评估节点支持的可靠性。本文的在线版本(DOI：10.1186/1471-2105-15-294)包含补充材料，授权用户可以使用。
Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree. We used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The approach implemented in AliGROOVE allows to detect nodes within a tree that are supported despite the absence of phylogenetic signal in the underlying multiple sequence alignment. We show that AliGROOVE equally well detects heterogeneous sequence divergence in a case study based on an empirical data set of mitochondrial DNA sequences of chelicerates. The AliGROOVE approach has the potential to identify single taxa or subsets of taxa which show predominantly randomized sequence similarity in comparison with other taxa in a multiple sequence alignment. It further allows to evaluate the reliability of node support in a novel way. The online version of this article (doi:10.1186/1471-2105-15-294) contains supplementary material, which is available to authorized users.
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影响因子：
4.1
作者：
Kueck, Patrick;Meusemann, Karen
通讯作者：
Meusemann, Karen
影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
6.5
作者：
Misof, Bernhard;Misof, Katharina
通讯作者：
Misof, Katharina
影响因子：
1.2
作者：
Dinapoli, Angela;Zinssmeister, Carmen;Klussmann-Kolb, Annette
通讯作者：
Klussmann-Kolb, Annette
影响因子：
3.4
作者：
Schwarzer, Julia;Misof, Bernhard;Schliewen, Ulrich K.
通讯作者：
Schliewen, Ulrich K.