AntibodyForests

AntibodyForests delineates inter- and intra-antibody repertoire evolution from single-cell V(D)J sequencing data by constructing lineage trees, comparing repertoire structures, and incorporating protein structure and evolutionary likelihood.

Key Features:

• Lineage tree construction: AntibodyForests infers B cell lineages from single-cell V(D)J sequencing data.
• Repertoire comparison: The software quantifies inter- and intra-antibody repertoire evolution.
• Somatic hypermutation analysis: AntibodyForests analyzes somatic hypermutation using protein language models and protein structure.
• Protein structure integration: The package incorporates protein structure into repertoire analyses.
• Evolutionary likelihood: AntibodyForests incorporates evolutionary likelihood into its analytical framework.

Scientific Applications:

• B cell evolution studies: AntibodyForests enables study of B cell repertoire evolution during immune responses at novel scale and resolution.
• Immune repertoire sequencing analysis: The software leverages single-cell technologies and artificial intelligence for immune repertoire sequencing data.

Methodology:

AntibodyForests uses protein language models and protein structure for somatic hypermutation analysis.