AFS	Coalescent-based
Type of data	SNPs (biallelic markers)	Phased DNA segment (haplotype)
Assumptions about recombination	Free recombination among SNPs (all SNPs independent)	Free recombination among loci, and complete linkage within loci
Assumptions about mutation	Mutation rates equal for all SNP	Mutation rates vary across loci
Likelihood	Diffusion-based or Coalescent-based	Coalescent-based
Methods	Composite -likelihoods. Relatively fast and able to deal with millions of SNPs.	Monte Carlo methods based on genealogy samplers (MCMC, Importance Sampling, etc.) or based on approximate methods (ABC, PAC). Usually slow and computationally intensive, compromising their application to large genomic datasets.