RESUMO
Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come.
RESUMO
Estimating Phylogenies of Species (EPoS) is a modular software framework for phylogenetic analysis, visualization and data management. It provides a plugin-based system that integrates a storage facility, a rich user interface and the ability to easily incorporate new methods, functions and visualizations. EPoS ships with persistent data management, a set of well-known phylogenetic algorithms and a multitude of tree visualization methods and layouts. Implemented algorithms cover distance-based tree construction, consensus trees and various graph-based supertree methods. The rendering system can be customized for, say, different edge and node styles.