Polynomial supertree methods in phylogenomics : algorithms, simulations and software
One of the objectives in modern biology, especially phylogenetics, is to build larger clades of the Tree of Life. Large-scale phylogenetic analysis involves several serious challenges. The aim of this thesis is to contribute to some of the open problems in this context. In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life. We present a novel polynomial time approach for the computation of supertrees called FlipCut supertree. Our method combines the computation of minimum cuts from graph-based methods with a matrix representation method, namely Minimum Flip Supertrees. Here, the input trees are encoded in a 0/1/?-matrix. We present a heuristic to search for a minimum set of 0/1-flips such that the resulting matrix admits a directed perfect phylogeny. In contrast to other polynomial time approaches, our results can be interpreted in the sense that we try to minimize a global objective function, namely the number of flips in the input matrix. We extend our approach by using edge weights to weight the columns of the 0/1/?-matrix. In order to compare our new FlipCut supertree method with other recent polynomial supertree methods and matrix representation methods, we present a large scale simulation study using two different data sets. Our findings illustrate the trade-off between accuracy and running time in supertree construction, as well as the pros and cons of different supertree approaches. Furthermore, we present EPoS, a modular software framework for phylogenetic analysis and visualization. It fills the gap between command line-based algorithmic packages and visual tools without sufficient support for computational methods. By combining a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations and data structures, we created a framework that is easy to use, to extend and that covers all important steps of a phylogenetic analysis.