Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

Motivation The rapid advancements in immune repertoire sequencing, powered by single-cell technologies and artificial intelligence, have created unprecedented opportunities to study B cell evolution at a novel scale and resolution. However, fully leveraging these data requires specialized software capable of performing inter- and intra-repertoire analyses to unravel the complex dynamics of B cell repertoire evolution during immune responses. Results Here, we present AntibodyForests, software to infer B cell lineages, quantify inter- and intra-antibody repertoire evolution, and analyze somatic hypermutation using protein language models and protein structure. Availability This R package is available on CRAN and Github at https://github.com/alexyermanos/AntibodyForests, a vignette is available at https://cran.case.edu/web/packages/AntibodyForests/vignettes/AntibodyForests_vignette.html Supplementary information Supplementary data are available at Bioinformatics online.