The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study.

ABSTRACT: The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This raises questions about how a set of sequences should be selected for analysis, particularly if the data are used to infer more than just the phylogenetic tree itself. The design of sampling strategies for molecular epidemiology has been a neglected field of research. This article describes a large-scale simulation exercise that was undertaken to select an appropriate strategy when using the GMRF skygrid, one of the Bayesian skyline family of coalescent methods, in order to reconstruct past populati

SUBMITTER: Hall MD 

PROVIDER: S-EPMC4989886 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature