# Delineating inter- and intra-antibody repertoire evolution with AntibodyForests

## TL;DR

AntibodyForests is a new software tool that helps researchers study how B cell antibody repertoires evolve using advanced computational methods.

## Contribution

AntibodyForests introduces a novel R package for analyzing B cell lineage and repertoire evolution using protein language models and structure.

## Key findings

- AntibodyForests enables lineage inference and quantification of repertoire evolution.
- The tool integrates protein language models and structural analysis for deeper insights.
- It supports both inter- and intra-repertoire comparisons during immune responses.

## Abstract

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.

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.

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.