Inferring gene duplications, transfers and losses can be done in a discrete framework

@article{Ranwez2016InferringGD,
  title={Inferring gene duplications, transfers and losses can be done in a discrete framework},
  author={Vincent Ranwez and C{\'e}line Scornavacca and Jean-Philippe Doyon and Vincent Berry},
  journal={Journal of Mathematical Biology},
  year={2016},
  volume={72},
  pages={1811-1844}
}
In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree—whose internal nodes represent speciation events—while the evolutionary history of a gene family is depicted by a gene tree—whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the… 
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