Abstract: Phylodynamics seeks to extract information on the transmission and evolution of a pathogen from genetic sequences. Mathematically, the problem boils down to that of constructing the likelihood function that links a dynamical system model to the genetic data. The two approaches to the problem currently in common use view the pathogen genealogy as a historical record of the generating process and rely on questionable assumptions and approximations. By taking a different viewpoint, from which we view the generative model as a genealogy-valued Markov process, we show that one can derive the likelihood without the need for questionable approximations and assumptions.
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