biostudies-literatureLuo JShenzhen Science and Technology Programbtaf346https://www.ebi.ac.uk/biostudies/studies/S-EPMC12282942biostudies-literatureUnknown41(7)<h4>Motivation</h4>B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumulation of advantageous mutations under successive rounds of somatic hypermutation (SHM) and selection, and are often incompatible with repertoire input.<h4>Results</h4>To address previous limitations, we developed AffMB (Affinity Maturation of B-cell receptor), a comprehensive toolkit for tracking affinity maturation through the generation and visualization of SHM-ordered, inheritance-based B-cell lineage trees from single-cell or bulk B-cell receptor sequencing data. The SHM-ordered inheritance tree algorithm outperformed state-of-the-art benchmarks in simulations. When applied to single-cell data from BNT162b2 vaccination (n = 42), AffMB demonstrated the ability to infer immunization responses and showed the feasibility of identifying potential high-affinity antibody sequences.<h4>Availability and implementation</h4>AffMB is an open-source Python package that supports contig FASTA or AIRR rearrangement TSV inputs. The source code for AffMB is freely available at https://github.com/deepomicslab/AffMB.Bioinformatics (Oxford, England)AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.PMC12282942JCYJ20200109143216036Zou YLuo JLi SCfalseAffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.<h4>Motivation</h4>B-cell lineage trees describe the evolutionary process of immunoglobulin genes during affinity maturation. Existing methods for building B-cell lineage trees generally do not guarantee the parent-to-child inheritance and accumulation of advantageous mutations under successive rounds of somatic hypermutation (SHM) and selection, and are often incompatible with repertoire input.<h4>Results</h4>To address previous limitations, we developed AffMB (Affinity Maturation of B-cell receptor), a comprehensive toolkit for tracking affinity maturation through the generation and visualization of SHM-ordered, inheritance-based B-cell lineage trees from single-cell or bulk B-cell receptor sequencing data. The SHM-ordered inheritance tree algorithm outperformed state-of-the-art benchmarks in simulations. When applied to single-cell data from BNT162b2 vaccination (n = 42), AffMB demonstrated the ability to infer immunization responses and showed the feasibility of identifying potential high-affinity antibody sequences.<h4>Availability and implementation</h4>AffMB is an open-source Python package that supports contig FASTA or AIRR rearrangement TSV inputs. The source code for AffMB is freely available at https://github.com/deepomicslab/AffMB.2025-01-01T00:00:00Z2025 Jul2026-03-27T16:21:14.467Z2025-08-30T03:05:57.728ZS-EPMC122829424067457910.1093/bioinformatics/btaf346