SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference …