Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

• Published in: PLoS computational biology Vol. 11; no. 12; p. e1004613
• Main Authors: Hall, Matthew, Woolhouse, Mark, Rambaut, Andrew
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.12.2015; Public Library of Science (PLoS)
• Subjects: Algorithms; Animals; Computational Biology - methods; Disease transmission; Epidemics; Epidemics - classification; Genetic aspects; Influenza A Virus, H7N7 Subtype - genetics; Influenza in Birds - epidemiology; Influenza in Birds - virology; Markov Chains; Methods; Models, Biological; Monte Carlo Method; Phylogenetic trees; Phylogenetics; Phylogeny; Poultry - virology; Software; Trees

The use of genetic data to reconstruct the transmission tree of infectious disease epidemics and outbreaks has been the subject of an increasing number of studies, but previous approaches have usually either made assumptions that are not fully compatible with phylogenetic inference, or, where they h...