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Article: Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

TitleExploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
Authors
KeywordsPhylogeny
Molecular clock
Evolutionary rate
Regression
Model selection
Issue Date2016
PublisherOxford University Press. The Journal's web site is located at http://ve.oxfordjournals.org
Citation
Virus Evolution, 2016, v. 2 n. 1, article no. UNSP vew007 How to Cite?
AbstractGene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis.
Persistent Identifierhttp://hdl.handle.net/10722/263780
ISSN
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorRambaut, A-
dc.contributor.authorLam, TY-
dc.contributor.authorMax Carvalho, L-
dc.contributor.authorPybus, OG-
dc.date.accessioned2018-10-22T07:44:22Z-
dc.date.available2018-10-22T07:44:22Z-
dc.date.issued2016-
dc.identifier.citationVirus Evolution, 2016, v. 2 n. 1, article no. UNSP vew007-
dc.identifier.issn2057-1577-
dc.identifier.urihttp://hdl.handle.net/10722/263780-
dc.description.abstractGene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://ve.oxfordjournals.org-
dc.relation.ispartofVirus Evolution-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectPhylogeny-
dc.subjectMolecular clock-
dc.subjectEvolutionary rate-
dc.subjectRegression-
dc.subjectModel selection-
dc.titleExploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)-
dc.typeArticle-
dc.identifier.emailLam, TY: ttylam@hku.hk-
dc.identifier.authorityLam, TY=rp01733-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/ve/vew007-
dc.identifier.pmid27774300-
dc.identifier.hkuros294140-
dc.identifier.volume2-
dc.identifier.issue1-
dc.identifier.spagearticle no. UNSP vew007-
dc.identifier.epagearticle no. UNSP vew007-
dc.identifier.isiWOS:000399949900011-
dc.publisher.placeUnited Kingdom-

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