About: Automated analysis of phylogenetic clusters

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Automated analysis of phylogenetic clusters
Creator	Ragonnet-Cronin, Manon Lycett, Samantha Delpech, Valerie Fearnhill, Esther Hodcroft, Emma Hué, Stéphane Brown, Andrew
Source	Medline; PMC
abstract	BACKGROUND: As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an automated Cluster Picker which identifies monophyletic clades meeting user-input criteria for bootstrap support and maximum genetic distance within large phylogenetic trees. A second tool, the Cluster Matcher, automates the process of linking genetic data to epidemiological or clinical data, and matches clusters between runs of the Cluster Picker. RESULTS: We explore the effect of different bootstrap and genetic distance thresholds on clusters identified in a data set of publicly available HIV sequences, and compare these results to those of a previously published tool for cluster identification. To demonstrate their utility, we then use the Cluster Picker and Cluster Matcher together to investigate how clusters in the data set changed over time. We find that clusters containing sequences from more than one UK location at the first time point (multiple origin) were significantly more likely to grow than those representing only a single location. CONCLUSIONS: The Cluster Picker and Cluster Matcher can rapidly process phylogenetic trees containing tens of thousands of sequences. Together these tools will facilitate comparisons of pathogen transmission dynamics between studies and countries.
has issue date	2013-11-06(xsd:dateTime)
bibo:doi	10.1186/1471-2105-14-317
bibo:pmid	24191891
has license	cc-by
sha1sum (hex)	7f8fc0ff30e4455d834e829db27b8d529b2920df
schema:url	https://doi.org/10.1186/1471-2105-14-317
resource representing a document's title	Automated analysis of phylogenetic clusters
has PubMed Central identifier	PMC4228337
has PubMed identifier	24191891
schema:publication	BMC Bioinformatics
resource representing a document's body	covid:7f8fc0ff30e4455d834e829db27b8d529b2920df#body_text
is schema:about of	named entity 'Cluster' named entity 'Automated' named entity 'phylogenetic' named entity 'Resistance' covid:arg/7f8fc0ff30e4455d834e829db27b8d529b2920df named entity 'Cluster' named entity 'automated' named entity 'matches' named entity 'monophyletic' named entity 'genetic distance' named entity 'data sets' named entity 'cluster analysis' named entity 'genetic distances' named entity 'recent common ancestor' named entity 'genetic distances' named entity 'HIV' named entity 'genetic distance' named entity 'sequence names' named entity 'bootstrap support' named entity 'genetic distance' named entity 'infection' named entity 'epidemiologically' named entity 'NCBI' named entity 'infection' named entity 'GenBank' named entity 'RNA viruses' named entity 'clustering coefficient' named entity 'genetic relatedness' named entity 'HIV' named entity 'pathogen' named entity 'posterior probability' named entity 'viruses' named entity 'Ebola' named entity 'infection' named entity 'pathogens' named entity 'HIV' named entity 'epidemic' named entity 'HCV' named entity 'HIV epidemic' named entity 'random graph' named entity 'infection' named entity 'HIV' named entity 'protease' named entity 'phylogenetic tree' named entity 'genetic distance' named entity 'Cluster' named entity 'bootstrap' named entity 'clusters' named entity 'cluster analysis' named entity 'genetic data' named entity 'automated tools' named entity 'phylogenetic' named entity 'HIV Drug Resistance Database' named entity 'phylogenetic' named entity 'disease transmission' named entity 'bootstrap support' named entity 'newick' named entity 'phylogenetic tree' named entity 'genetic distance' named entity 'HIV' named entity 'dengue' named entity 'GNU GPLv3' named entity 'genetic distance' named entity 'influenza' named entity 'drug treatment' named entity 'shortest path' named entity 'sequence clustering' named entity 'genetic distance' named entity 'ac.uk' named entity 'genetic distances' named entity 'genetic distance' named entity 'algorithm' named entity 'severe acute respiratory syndrome' named entity 'risk group' named entity 'genetic distance'

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