COSPEDTree-II: Improved Couplet based Phylogenetic Supertree

Abstract

A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard. Various heuristics on local search, maximum parsimony, graph cut, etc. lead to different supertree approaches, of which the most popular methods are based on analyzing fixed size subtree topologies (such as triplets or quartets). Time and space complexities of these methods, however, depend on the subtree size considered. Our earlier proposed supertree method COSPEDTree, uses evolutionary relationship among individual couplets (taxa pair), to produce slightly conservative (not fully resolved) supertrees. Here we propose its improved version COSPEDTree-II, which produces better resolved supertree with lower number of missing branches, and incurs much lower running time. Results on biological datasets show that COSPEDTree-II belongs to the category of high performance and computationally efficient supertree methods.