msprime

msprime simulates ancestral genealogies and DNA sequence variation using backwards-in-time coalescent models to enable scalable, exact coalescent simulations with recombination over chromosome-sized regions for large sample sizes.

Key Features:

• Efficient simulation: Employs backwards-in-time coalescent models to perform exact coalescent simulations with recombination over chromosome-sized regions for hundreds of thousands of samples.
• Sparse trees and coalescence records: Represents genealogies using sparse trees and coalescence records to reduce memory usage and accelerate computation.
• Long-range linkage properties: Preserves long-range linkage patterns that are not captured by many approximation-based simulators.
• Analytical performance: Enables rapid parsing and analysis by leveraging shared structure across correlated trees, providing orders-of-magnitude faster downstream analysis.

Scientific Applications:

• Population genetics: Simulates large-scale genetic variation and genealogies for inference and hypothesis testing in population genetics.
• Evolutionary biology: Models complex ancestral histories and recombination-driven evolutionary processes across chromosome-sized regions.
• Genomic research: Generates realistic genome-scale sequence data and genealogies for analyses that require very large sample sizes.

Methodology:

Backwards-in-time coalescent simulation with recombination using sparse tree and coalescence record representations to simulate chromosome-sized regions and enable rapid parsing of shared structure in correlated trees.