International Journal of Plant Genomics 
Volume 2008 (2008), Article ID 683509, 16 pages
doi:10.1155/2008/683509
Review Article

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

Stéphane Aris-Brosou1,2 and Xuhua Xia1

 1Department of Biology, Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ontario K1N 6N5, Canada
2Department of Mathematics and Statistics, University of Ottawa, Ontario K1N 6N5, Canada
Received 30 November 2007; Accepted 12 February 2008

Recommended by Chunguang Du

Abstract

The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesian methods are under heavy development as they offer the possibility to solve a number of long-standing issues and to integrate several steps of the phylogenetic analyses into a single framework. Specific topics include not only phylogenetic reconstruction, but also the comparison of phylogenies, the detection of adaptive evolution, and the estimation of divergence times between species.