mbs

mbs simulates patterns of single nucleotide polymorphisms (SNPs) in genomic regions linked to biallelic sites under natural selection using a modified coalescent framework.

Key Features:

• Incorporation of natural selection: Introduces selection acting on biallelic sites into coalescent simulations derived from Hudson's ms.
• Flexible demographic histories: Simulates DNA sequences under arbitrary histories of population size change.
• Multiple modes of selection: Supports various modes of selection to model different selective pressures on genetic variation.

Scientific Applications:

• Selection impact analysis: Evaluate how different selective regimes shape SNP patterns in genomic regions linked to biallelic sites.
• Demographic effects on variation: Assess how historical population size changes influence the distribution of SNPs.
• Testing evolutionary hypotheses: Test hypotheses of adaptive evolution and speciation by generating simulated DNA sequence datasets.

Methodology:

Modifies Hudson's ms within the coalescent theory framework to introduce selection on biallelic sites and generates large samples of DNA sequences.