“…Furthermore, there exist several methods to construct phylogenetic trees, including distance-based metrics, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (Stamatakis, 2006;Gascuel, 2006;Bouckaert et al, 2014). While there exist multiple simulation tools capable of exploring how inference method impacts the resulting phylogenetic trees derived from simulated B cell data (Yermanos et al, 2017;Davidsen and Matsen IV, 2018;Safonova et al, 2015;Weber et al, 2019), the extent of this influence on the evolutionary conclusions on experimental data remains largely unexplored. It remains unknown, for example, the extent of which the phylogenetic inference strategy impacts the biological conclusions pertaining to the evolutionary landscape across various infection cohorts.…”