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

Zhemin Zhou; Nabil-Fareed Alikhan; Martin J. Sergeant; Nina Luhmann; Cátia Vaz; Alexandre P. Francisco; João André Carriço; Mark Achtman

doi:10.1101/gr.232397.117

BioinformaticsGenome ResearchSep 1, 2018

Peer-reviewed journal article

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

Zhemin Zhou iD, Nabil-Fareed Alikhan iD, Martin J. Sergeant iD, Nina Luhmann iD, Cátia Vaz iD, Alexandre P. Francisco iD, João André Carriço iD, Mark Achtman iD

Abstract

O_LICurrent methods struggle to reconstruct and visualise the genomic relationships of [≥]100,000 bacterial genomes.\nC_LIO_LIGrapeTree facilitates the analyses of allelic profiles from 10,000s of core genomes within a web browser window.\nC_LIO_LIGrapeTree implements a novel minimum spanning tree algorithm to reconstruct genetic relationships despite missing data together with a static \"GrapeTree Layout\" algorithm to render interactive visualisations of large trees.\nC_LIO_LIGrapeTree is a stand-along package for investigating Newick trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among >160,000 genomes from bacterial pathogens.\nC_LIO_LIThe GrapeTree package was released under the GPL v3.0 Licence.\nC_LI

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