Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically.

{"references": ["Yermanos A, et al. (2017) Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). Bioinformatics. 33(24):3938\u20133946."]}