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dc.contributor.author
Barrat-Charlaix, Pierre
dc.contributor.author
Vaughan, Timothy G.
dc.contributor.author
Neher, Richard A.
dc.date.accessioned
2022-09-26T09:19:31Z
dc.date.available
2022-09-25T03:15:12Z
dc.date.available
2022-09-26T09:17:37Z
dc.date.available
2022-09-26T09:19:31Z
dc.date.issued
2022-08
dc.identifier.issn
1553-734X
dc.identifier.issn
1553-7358
dc.identifier.other
10.1371/journal.pcbi.1010394
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/572566
dc.identifier.doi
10.3929/ethz-b-000572566
dc.description.abstract
When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
PLOS
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Phylogenetic analysis
en_US
dc.subject
Leaves
en_US
dc.subject
Trees
en_US
dc.subject
Influenza viruses
en_US
dc.subject
Influenza
en_US
dc.subject
Viral evolution
en_US
dc.subject
Graphs
en_US
dc.subject
Optimization
en_US
dc.title
TreeKnit: Inferring ancestral reassortment graphs of influenza viruses
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2022-08-19
ethz.journal.title
PLoS Computational Biology
ethz.journal.volume
18
en_US
ethz.journal.issue
8
en_US
ethz.journal.abbreviated
PLOS comput. biol.
ethz.pages.start
e1010394
en_US
ethz.size
19 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
San Francisco, CA
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.date.deposited
2022-09-25T03:15:13Z
ethz.source
SCOPUS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2022-09-26T09:17:38Z
ethz.rosetta.lastUpdated
2024-02-02T18:19:56Z
ethz.rosetta.versionExported
true
ethz.COinS
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