QT-WEAVER: Correcting quartet distribution improves phylogenomic analyses despite gene tree estimation error

Summarizing individual gene trees into species phylogenies using coalescent-based methods has become a standard approach in phylogenomics. However, gene tree estimation error (GTEE) arising from a combination of reasons (ranging from analytical factors to more biological causes, as in short gene sequences) can potentially impact the accuracy of phylogenomic inference. We, for the first time, introduce the problem of correcting the quartet distribution induced by a set of estimated gene trees, which involves updating the weights of the quartets to better reflect their relative importance within the gene tree distribution. We present QT-WEAVER, the first method of its kind, which learns the conflicts within the quartet distribution induced by a given set of gene trees and generates an updated quartet distribution by adjusting the weights accordingly. QT-WEAVER is a general-purpose technique needing no explicit modeling of the subject system or reasons for GTEE or gene tree heterogeneity. Experimental studies on a collection of simulated and empirical data sets suggest that QT-WEAVER can effectively account for GTEE, which results in a substantial improvement in the species tree accuracy. Additionally, the concept of quartet conflicts and related algorithmic and combinatorial innovations introduced in this study will benefit various quartet-based computations. Therefore, QT-WEAVER advances the state-of-the-art in species tree estimation from gene trees in the face of GTEE. QT-WEAVER is freely available in open-source form at https://github.com/navidh86/QT-WEAVER.