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  • Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). SCOTTI is distributed as an open source package for the phylogenetic software BEAST2. Here, we present a new approach, SCOTTI, that accounts for these complexities in a computationally feasible manner. SCOTTI is implemented as an open-source package for the Bayesian phylogenetic software BEAST2 [28], and as such, it can be freely installed and used.
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