GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
- Zhemin Zhou1,
- Nabil-Fareed Alikhan1,
- Martin J. Sergeant1,
- Nina Luhmann1,
- Cátia Vaz2,3,
- Alexandre P. Francisco2,4,
- João André Carriço5 and
- Mark Achtman1
- 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
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.232397.117.
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Freely available online through the Genome Research Open Access option.
- Received November 14, 2017.
- Accepted July 24, 2018.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
