Journal article

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

Sebastian Duchene, David Duchene, Jemma Geoghegan, Zoe Anne Dyson, Jane Hawkey, Kathryn Holt

Published : 2017


Background: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, w..

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