Models of RNA virus evolution and their roles in vaccine design

Ojosnegros, Samuel; Beerenwinkel, Niko

Unlike distance-based methods, character-based methods follow character substitutions in the sequence explicitly. Maximum Parsimony is based on the minimum evolution principle and tries to find the tree that explains the data by the minimum number of mutations [83] . The method has been applied successfully to the analysis of influenza virus sequence data [84] . It is also computationally efficient, but lacks an explicit evolutionary model (other than minimum evolution), and it is not statistically consistent. On the other hand, probabilistic phylogenetic models have these desirable properties, but they come at a computational cost usually rendering exact maximum likelihood estimation impossible. However, approximate likelihood methods, such as DNAML [59] or QuartetPuzzling [85] , and methods making use of Bayesian inference, such as MrBayes [86] are applied in practice. For both distance-based methods and probabilistic phylogenetic methods, the choice of an appropriate model of nucleotide substitution is critical.