What is a hidden Markov model?

@article{Eddy2004WhatIA,
  title={What is a hidden Markov model?},
  author={Sean R. Eddy},
  journal={Nature Biotechnology},
  year={2004},
  volume={22},
  pages={1315-1316}
}
Population structure • Simulated descent and recombination in a population of 7,000 individuals over 200 generations • Chromosomes represented as mosaics of founder chromosomes • 500 pairs of individuals from final generation sampled Background LD • For marker data, fit LD model to Framingham Heart Study haplotypes using BEAGLE • Generated new haplotypes by sampling from fitted model, with additional recombination (γ) introduced to control level of LD 
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