GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees wi...

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Bibliographic Details
Published in:Genome research Vol. 28; no. 9; p. 1395
Main Authors: Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J, Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P, Carriço, João André, Achtman, Mark
Format: Journal Article
Language:English
Published: United States 01.09.2018
Subjects:
Alleles
Bacteria - classification
Bacteria - genetics
Bacteria - pathogenicity
DNA Barcoding, Taxonomic - methods
Genome, Bacterial
Phylogeny
Software
ISSN:1549-5469, 1549-5469
Online Access:Get more information
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Summary:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.
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ISSN:1549-5469
1549-5469
DOI:10.1101/gr.232397.117