Data from: Weighted quartets phylogenetics

Despite the impressive advancements in technology as well as in theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. In particular, the presence of enormous quantities of molecular data available for taxonomic classication, has drawn the attention to large scale phylogenetic reconstruction. A key tool in this direction is the construction of separate trees over dierent, overlapping subsets of the species, and subsequently combine these trees into a single tree over the full set. A quartet tree - a tree over four species, is the most basic informational phylogenetic unit. The amalgamation of such quartets into a single tree lies at heart of many tasks in phylogenetics, yet remained a daunting task, in particular in light of conicting signals - a common reality in biology. Assigning these quartets with weights to indicate importance or reliability has been proposed more than a decade ago. Handling weighted quartets is even more challenging and was scarcely dealt in the past. In this work we focus on weighted quartet based approaches. We propose a scheme to assign weights to quartets coming from weighted trees and devise a tree similarity measure for weighted trees based on weighted quartets. We also extend the quartet MaxCut (QMC algorithm to handle weighted quartets using the tools above. We evaluated these tools by extensive experiments, both on simulated and real data and confronted the weighted QMC (wQMC) with the most prevalent tool - MRP. Our results show that wQMC is signicantly superior to MRP by all measures. Our real data results on cyanobacterial gene trees enforces previous results achieved by other tools.