Method

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

    • 1Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom;
    • 2Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), 1000-029 Lisboa, Portugal;
    • 3ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, 1959-007 Lisboa, Portugal;
    • 4Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
    • 5Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-004 Lisboa, Portugal
Published July 26, 2018. https://doi.org/10.1101/gr.232397.117
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cover of Genome Research Vol 36 Issue 6
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June 2026, Vol. 36, No. 6
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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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