PANPROVA

PANPROVA: Whole-Genome Pangenome Evolution Simulator

PANPROVA simulates evolution of entire genomes from an ancestral isolate, generating complete genomic datasets for pangenomic analysis and benchmarking.

Key Features:

• Complete Genomic Simulation: Evolves full genomes from an ancestral isolate, preserving complete genomic information for pangenome analysis.
• Pre-Assembly Operation: Simulates evolutionary processes prior to genome assembly to model variation in fragmented genomic states.
• Gene Set Variations: Incorporates gene presence and absence variation across strains.
• Sequence Variation: Models mutations and genomic alterations over evolutionary time.
• Horizontal Gene Acquisition: Simulates gene transfer from external genome pools to reflect prokaryotic evolutionary dynamics.

Scientific Applications:

• Pangenomic Benchmarking: Generates synthetic genomic datasets for evaluation of pangenomic analysis tools and supports studies of genomic diversity and vaccine development.

Methodology:

Evolves ancestral isolate genomes by integrating gene presence and absence variation, sequence-level mutations, and horizontal gene acquisition from external genome pools to produce simulated pangenomic evolution datasets.