Probabilistic Inference of Viral Quasispecies Subject to Recombination

@article{Tpfer2013ProbabilisticIO,
  title={Probabilistic Inference of Viral Quasispecies Subject to Recombination},
  author={Armin T{\"o}pfer and Osvaldo Zagordi and Sandhya Prabhakaran and Volker Roth and Eran Halperin and Niko Beerenwinkel},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2013},
  volume={20 2},
  pages={113-23}
}
RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral quasispecies and a method to infer its parameters from next-generation sequencing data. The model introduces position-specific probability tables… CONTINUE READING
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