Phylogenetic inference package IgPhyML is a tool designed for B cell repertoires. It incorporates unique features of somatic hypermutation into the codon substitution models it implements, allowing for parameter estimation across lineages to characterize entire repertoires. This software provides an efficient and accurate way to analyze phylogenetic relationships between different organisms and their associated immune systems.IgPhyML is a phylogenetic inference package for B cell repertoires. It implements codon substitution models designed that incorporate unique features of somatic hypermutation and allow for parameter estimation across lineages to characterize entire repertoires.