simurg

simurg simulates bacterial pangenomes within R under defined evolutionary models to enable study of pangenome variability and structure.

Key Features:

• Evolutionary model simulation: Simulates bacterial pangenomes under defined evolutionary constraints including gene gain, gene loss, and mutation rates.
• Reproducible simulations for benchmarking: Produces reproducible simulations using real sequence data to benchmark pangenome analysis software.
• Integration with real sequence data: Performs simulations based on actual sequence data to reflect realistic genetic variability and pangenome structure.
• R implementation: Implements simulation functionality as an R package.

Scientific Applications:

• Benchmarking pangenome software: Tests and validates the performance of pangenome analysis tools under varied evolutionary scenarios.
• Comparative evolutionary studies: Explores the effects of gene gain, gene loss, and mutation rates on bacterial diversity and pangenome composition.

Methodology:

Simulations are executed within R under defined evolutionary models (gene gain, gene loss, mutation rates) and can be parameterized or driven by real sequence data to produce reproducible datasets for benchmarking.