AbSim

AbSim simulates time-resolved antibody repertoire evolution to generate realistic B-cell lineage sequences for evaluating and comparing phylogenetic reconstruction methods.

Key Features:

• Time-resolved simulation: Simulates both single lineages using specific sets of V-, D-, and J-genes and full antibody repertoires across evolutionary time.
• Intermediate-stage modeling: Generates intermediate antibody sequence states to represent evolutionary progression over time.
• Immunologically relevant parameters: Incorporates parameters such as duration of repertoire evolution and mutation methods and frequency.
• Topology replication: Produces simulated trees that replicate topological similarities observed in experimental sequencing data.
• Phylogenetic assessment: Enables demonstration and analysis of cases where existing phylogenetic methods fail to recover true evolutionary trees.

Scientific Applications:

• Phylogenetic method benchmarking: Tests the accuracy of phylogenetic reconstruction methods for B-cell lineages and antibody molecular evolution.
• Validation against experimental data: Provides simulated datasets for comparing inferred trees and sequences to experimental sequencing observations.
• Guideline development: Supports formulation of simulation-validated guidelines for interpreting antibody evolution and improving phylogenetic approaches.

Methodology:

Computationally generates antibody sequences and phylogenies calibrated to replicate topological patterns from experimental sequencing data and uses these simulations to validate phylogenetic inference accuracy.