Abstract
Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets.
Highlights
A phylogenetic tree of a group of species describes the evolutionary relationship among the species
We have evaluated the accuracy of the trees estimated by Quartet Fiduccia and Mattheyses (FM) (QFM) and compared the results to that of quartet max-cut (QMC) [9]
RF rate is the mostly used error metric, which is the ratio of the sum of the number of false positive and false negative edges to a factor 2n{6, where n is the number of taxa [1]
Summary
A phylogenetic tree of a group of species (taxa) describes the evolutionary relationship among the species. Phylogenetic tree reconstruction by analyzing the molecular sequences of different species can be regarded as the sequencebased reconstruction of the phylogeny. As a result, these can only be applied on small to moderate sized datasets if we want to provide results having an acceptable level of accuracy within a moderate amount of time. For larger datasets (few hundreds of taxa (species)), these methods may need several weeks or months to provide results with an acceptable level of accuracy [1]. We are forced to rely on supertree methods, where smaller trees on overlapping groups of species are combined together to get a single larger tree. Supertree-based tree construction is a two-phase method: in the first phase, many small trees on overlapping subsets of taxa are constructed using a sequence-based method; and in the phase the small trees are summarized into a complete tree over the full set of taxa
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