The double-edged complexity of molecular sequence evolution

Abstract

Traditionally, phylogenetic studies based on sequence data assume simple models of evolution. This is due to computational and time constraints and to our incomplete understanding of the actual complexity of the evolutionary process. The importance of producing tools and protocols to manage this complexity is twofold; to improve the efficacy of phylogenetic reconstruction methods, and to detect peculiarities of the evolutionary process that may lead to biologically interesting conclusions and predictions.