A general method for calculating likelihoods under the coalescent process.

@article{Lohse2011AGM,
  title={A general method for calculating likelihoods under the coalescent process.},
  author={K Lohse and Richard John Patrick Harrison and Nicholas H. Barton},
  journal={Genetics},
  year={2011},
  volume={189 3},
  pages={977-87}
}
Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any… CONTINUE READING
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