Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods
Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods
复制标题
DOI：
10.1109/tcbb.2016.2638911
复制
发表时间：
2018-05-01
影响因子：
4.5
通讯作者：
Weber, Noah
中科院分区：
文献类型：
--
作者：
Davidson, Ruth;Lawhorn, MaLyn;Weber, Noah
长期以来，由较大的系统发育树显示的四元树一直被用作物种树和超树重建的输入。由于计算的限制，在许多具有大量分类群的实际问题中，无法使用所有显示的四元组。我们引入了有效的四元组系统(EQS)的概念来表示具有由该树显示的四元组的子集的系统发育树。我们从数学上证明了通过方程从树上得到的四元组集合包含了树本身的所有组合信息。通过在模拟数据集上的性能测试，我们还证明了使用EQS来减少物种树推理的摘要方法流水线和超树推理方法中的四位数只会导致精度的微小下降。
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all displayed quartets inmany practical problems with large numbers of taxa. We introduce the notion of an Efficient Quartet System(EQS) to represent a phylogenetic tree with a subset of the quartets displayed by the tree. We show mathematically that the set of quartets obtained from a tree via an EQScontains all of the combinatorial information of the tree itself. Using performance tests on simulated datasets, we also demonstrate that using an EQS to reduce the number of quartets in both summary method pipelines for species tree inference as well as methods for supertree inference results in only small reductions in accuracy.