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

Zhemin Zhou, View ORCID ProfileNabil-Fareed Alikhan, View ORCID ProfileMartin J. Sergeant, View ORCID ProfileNina Luhmann, View ORCID ProfileCátia Vaz, View ORCID ProfileAlexandre P. Francisco, João André Carriço, View ORCID ProfileMark Achtman
doi: https://doi.org/10.1101/216788
Zhemin Zhou
Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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  • For correspondence: zhemin.zhou@warwick.ac.uk M.J.Sergeant@warwick.ac.uk
Nabil-Fareed Alikhan
Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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  • ORCID record for Nabil-Fareed Alikhan
Martin J. Sergeant
Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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  • ORCID record for Martin J. Sergeant
  • For correspondence: zhemin.zhou@warwick.ac.uk M.J.Sergeant@warwick.ac.uk
Nina Luhmann
Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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  • ORCID record for Nina Luhmann
Cátia Vaz
Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, PortugalADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
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  • ORCID record for Cátia Vaz
Alexandre P. Francisco
Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, PortugalInstituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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João André Carriço
Universidade de Lisboa, Faculdade de Medicina, Instituto de Microbiologia and Instituto de Medicina Molecular, Lisboa, Portugal
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Mark Achtman
Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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  • ORCID record for Mark Achtman
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Abstract

  1. Current methods struggle to reconstruct and visualise the genomic relationships of ≥100,000 bacterial genomes.

  2. GrapeTree facilitates the analyses of allelic profiles from 10,000’s of core genomes within a web browser window.

  3. GrapeTree 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.

  4. GrapeTree 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.

  5. The GrapeTree package was released under the GPL v3.0 Licence.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 09, 2017.
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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
bioRxiv 216788; doi: https://doi.org/10.1101/216788
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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
bioRxiv 216788; doi: https://doi.org/10.1101/216788

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