Davidson Ruth, Lawhorn MaLyn, Rusinko Joseph, Weber Noah
IEEE/ACM Trans Comput Biol Bioinform. 2018 May-Jun;15(3):1010-1015. doi: 10.1109/TCBB.2016.2638911. Epub 2016 Dec 14.
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 in many 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 EQS contains 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.
较大的系统发育树所展示的四重奏树长期以来一直被用作物种树和超树重建的输入。计算限制使得在许多包含大量分类单元的实际问题中无法使用所有展示的四重奏。我们引入了高效四重奏系统（EQS）的概念，用树所展示的四重奏子集来表示系统发育树。我们通过数学证明，通过EQS从树中获得的四重奏集合包含了树本身的所有组合信息。通过对模拟数据集的性能测试，我们还证明，在物种树推断的汇总方法流程以及超树推断方法中，使用EQS来减少四重奏的数量只会导致准确性有小幅下降。
