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

Zhou, Zhemin; Alikhan, Nabil-Fareed; Sergeant, Martin; Luhmann, Nina; Vaz, Cátia; Francisco, Alexandre; Carrico, Joao; Achtman, Mark

http://hdl.handle.net/10400.21/9099

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Authors

Zhou, Zhemin

Alikhan, Nabil-Fareed

Abstract(s)

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.

Keywords

Bacterial genome GrapeTree Genoma bacteriano

URI

http://hdl.handle.net/10400.21/9099

Citation

ZHEMIN, Zhou; [et al] – GrapeTree visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research. ISSN 1088-9051. Vol. 28, N.º 9 (2018), pp. 1395-1404