Continuous and tractable models for the variation of evolutionary rates.

@article{Lepage2006ContinuousAT,
  title={Continuous and tractable models for the variation of evolutionary rates.},
  author={Thomas Lepage and Stephan Lawi and Paul Tupper and David Bryant},
  journal={Mathematical biosciences},
  year={2006},
  volume={199 2},
  pages={216-33}
}
We propose a continuous model for variation in the evolutionary rate across sites and over the phylogenetic tree. We derive exact transition probabilities of substitutions under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in financial applications. The model directly extends the standard gamma distributed rates across site model, with one additional parameter governing changes in rate down the tree. The parameters of the model can be estimated… CONTINUE READING
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