A hidden Markov model for investigating recent positive selection through haplotype structure.

@article{Chen2015AHM,
  title={A hidden Markov model for investigating recent positive selection through haplotype structure.},
  author={Hua Chen and Jody Hey and Montgomery Slatkin},
  journal={Theoretical population biology},
  year={2015},
  volume={99},
  pages={18-30}
}
Recent positive selection can increase the frequency of an advantageous mutant rapidly enough that a relatively long ancestral haplotype will be remained intact around it. We present a hidden Markov model (HMM) to identify such haplotype structures. With HMM identified haplotype structures, a population genetic model for the extent of ancestral haplotypes is then adopted for parameter inference of the selection intensity and the allele age. Simulations show that this method can detect selection… CONTINUE READING

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