![]() ![]() ![]() 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 next phase the small trees are summarized into a complete tree over the full set of taxa. ![]() Therefore, 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. As the amount of molecular data is accumulating exponentially with the continuous advancement in sequencing technologies, scientists are facing new computational challenges to analyze these enormous amount of data. 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. 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. However, these methods are computationally intensive. Sequence-based methods are generally highly accurate. Sequence-based phylogenetic methods are basically of three types : (a) distance-based methods, such as Neighbor Joining (NJ), which has very fast practical performance (b) heuristics for either Maximum-Likelihood (ML) or Maximum-Parsimony (MP), which are two NP hard optimization problems and (c) the Bayesian Markov Chain Monte Carlo (MCMC) method, which, instead of a single tree, produces a probability distribution of the trees or aspects of the evolutionary history. Phylogenetic tree reconstruction by analyzing the molecular sequences of different species can be regarded as the sequence-based reconstruction of the phylogeny. The ultimate goal of this research community is to infer the Tree of Life, the phylogeny of all living organisms on earth, provided that it exists. The study of phylogeny not only helps to identify the historical relationships among a group of organisms, but also supports some other biological research such as drug and vaccine design, protein structure prediction, multiple sequence alignment and so on. A phylogenetic tree of a group of species (taxa) describes the evolutionary relationship among the species. ![]()
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