Phylogenetics: Applications, Software and Challenges

Abstract

Inference of phylogenetic trees comprising hundreds of organisms based on elaborate statistical models of evolution is an intensive computational task. However, in recent years there has been an impressive improvement in search algorithms, which currently allow for inference of huge phylogenetic trees comprising more than 1,000 taxa within a couple of hours on a single PC. This paper provides an overview of applications of phylogenetic trees to various areas of biological and medical research and reviews some of the most efficient software available for phylogenetic inference. Finally, some of the new challenges that the field currently faces in the areas of high performance computing and information visualization are discussed.