ClonalTree

ClonalTree reconstructs B cell lineage trees by integrating genotype abundances into minimum spanning tree (MST) algorithms to analyze B cell receptor (BCR) gene evolution during somatic hypermutations and Darwinian antigen selection in affinity maturation.

Key Features:

• Incorporation of Genotype Abundances: Integrates cellular genotype abundances into MST-based algorithms to represent clonal expansion and selection within B cell populations.
• Minimum Spanning Tree (MST) Framework: Uses MST algorithms as the core computational approach for reconstructing lineage relationships among BCR sequences.
• Efficiency and Accuracy: Employs a low-complexity algorithm that is reported to outperform traditional MST-based methods and achieve performance comparable to exhaustive tree-generating approaches while reducing computational time by hundreds to thousands of times.
• High-Throughput Compatibility: Enables rapid construction of B cell lineage trees from high-throughput BCR sequencing data within minutes or seconds for large datasets.
• Validation on Diverse Data: Has been validated using both simulated and experimental datasets to demonstrate robustness across data types.

Scientific Applications:

• Affinity Maturation Studies: Supports analysis of antibody affinity maturation by mapping mutation trajectories and selection patterns in BCR sequences.
• Clonal Selection Analysis: Enables investigation of clonal expansion and selection dynamics within B cell populations using genotype abundance information.
• B Cell Lineage Reconstruction: Reconstructs lineages that include unmutated ancestors and mutated variants to characterize evolutionary events in B cell repertoires from large-scale sequencing data.

Methodology:

Integrates genotype abundances into minimum spanning tree (MST) algorithms to reconstruct lineage trees that reflect BCR affinity maturation dynamics.