title: Why should we care about molecular coevolution?
abstract: Non-independent evolution of amino acid sites has become a noticeable limitation of most methods aimed at identifying selective constraints at functionally important amino acid sites or protein regions. The need for a generalised framework to account for non-independence of amino acid sites has fuelled the design and development of new mathematical models and computational tools centred on resolving this problem. Molecular coevolution is one of the most active areas of research, with an increasing rate of new models and methods being developed everyday. Both parametric and non-parametric methods have been developed to account for correlated variability of amino acid sites. These methods have been utilised for detecting phylogenetic, functional and structural coevolution as well as to identify surfaces of amino acid sites involved in protein-protein interactions. Here we discuss and briefly describe these methods, and identify their advantages and limitations.
authors.affiliation: Evolutionary Genetics and Bioinformatics Laboratory, Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Codoñer
authors.forename: Mario A
authors.initials: MA
authors.lastname: Fares