Work

Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods

Year: 2016

Type: article

Abstract: 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.

Source: IEEE Transactions on Computational Biology and Bioinformatics

DOI: 10.1109/tcbb.2016.2638911

Authors: Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko, Noah Weber

Institutions: University of Illinois Urbana-Champaign, Winthrop University, Hobart and William Smith Colleges

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences, National Center for Research Resources