Bayesian Phylogenetics

An immune response produces antibodies to remove infectious material in the human body. A "slow" evolutionary process, called clonal selection, uses natural selection to identify a binding match between antibody and antigen receptors. One identification strategy uses an ancestral tree, called phylogenetic tree reconstruction, to infer candidate antibodies. For reconstructive inference, many software tools use Bayesian MCMC methods and assume a simplified antibody mutation process, lacking biological realism. This analysis investigates reconstructive performance for two established tools under different mutation models via simulation study. Poor inference accuracy under a misspecified mutation model could warrant additional study of evolutionary modeling and a better understanding of antibody mutation would provide researchers with the capability to develop vaccines faster, cheaper and more effectively.