Multipolar consensus for phylogenetic trees
Multipolar consensus for phylogenetic trees
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DOI：
10.1080/10635150600969880
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发表时间：
2006-01-01
影响因子：
6.5
通讯作者：
Lartillot, Nicolas
中科院分区：
文献类型：
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作者：
Bonnard, Cecile;Berry, Vincent;Lartillot, Nicolas
系统发育树的集合通常使用一致的方法进行总结。这些方法构建单个树，被认为是集合的代表。然而，在树的不同集合的情况下，所产生的共识可能解决得不好(严格的共识、多数规则的共识，...)，或者可能在相互不兼容的分支或分裂(贪婪的共识)中执行任意选择。这里，我们提出了另一种方法，我们称之为多极共识(MPC)。它的目的是在最小数量的共识树或极点中显示支持度高于预定义阈值的所有拆分。我们证明了该问题等价于图着色问题，并给出了该方法的一个实现。最后，我们将预测控制应用于实际数据集。我们的结果表明，通常情况下，所有拆分到10%的权重可以显示在不超过4棵树中。此外，在某些情况下，我们的方法确实捕捉到了在任何经典共识树中都不存在的生物相关的二级信号，这表明MPC为系统发育分析提供了一种方便的探索性方法。该方法是在cbonnard/mpc.html的http://www.lirmm.fr/similar上免费获得的包中实现的。
Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of heterogeneous collections of trees, the resulting consensus may be poorly resolved ( strict consensus, majority-rule consensus,...), or may perform arbitrary choices among mutually incompatible clades, or splits ( greedy consensus). Here, we propose an alternative method, which we call the multipolar consensus ( MPC). Its aim is to display all the splits having a support above a predefined threshold, in a minimum number of consensus trees, or poles. We show that the problem is equivalent to a graph-coloring problem, and propose an implementation of the method. Finally, we apply the MPC to real data sets. Our results indicate that, typically, all the splits down to a weight of 10% can be displayed in no more than 4 trees. In addition, in some cases, biologically relevant secondary signals, which would not have been present in any of the classical consensus trees, are indeed captured by our method, indicating that the MPC provides a convenient exploratory method for phylogenetic analysis. The method was implemented in a package freely available at http://www.lirmm.fr/similar to cbonnard/MPC.html.