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

Matthew Hall; Mark Woolhouse; Andrew Rambaut

doi:10.1371/journal.pcbi.1004613

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Open Access

Peer-reviewed

Research Article

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

Matthew Hall ,

* E-mail: m.d.hall@sms.ed.ac.uk

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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Mark Woolhouse,

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
⨯
Andrew Rambaut

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
⨯

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

Matthew Hall,
Mark Woolhouse,
Andrew Rambaut

Published: December 30, 2015
https://doi.org/10.1371/journal.pcbi.1004613

About the Authors

Matthew Hall

* E-mail: m.d.hall@sms.ed.ac.uk

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom

Mark Woolhouse

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom

Andrew Rambaut

Affiliations Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: MH MW AR. Performed the experiments: MH. Analyzed the data: MH. Contributed reagents/materials/analysis tools: AR. Wrote the paper: MH AR MW.

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Phylogenetic analysis
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Phylogenetics
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Farms
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Genetic epidemiology
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Pathogens
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Animal phylogenetics
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Probability distribution
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Epidemiology
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