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Updated: Feb 7, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
Zhemin Zhou1, Nabil-Fareed Alikhan1, Martin J Sergeant1
1Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom.
Abstract:
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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