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GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens
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Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Catia, Francisco, Alexandre P., Carrico, Joao Andre and Achtman, Mark (2017) GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens. Working Paper. BioRxiv: Cold Spring Harbour.
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WRAP-GrapeTree-visualisation-core-genomic-relationships-bacterial-Alikhan-2017.pdf - Accepted Version - Requires a PDF viewer. Available under License Creative Commons: Attribution-Noncommercial 4.0. Download (5Mb) | Preview |
Official URL: http://dx.doi.org/10.1101/216788
Abstract
Current methods struggle to reconstruct and visualise the genomic relationships of ≥100,000 bacterial genomes. GrapeTree facilitates the analyses of allelic profiles from 10,000's of core genomes within a web browser window. 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. 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. The GrapeTree package was released under the GPL v3.0 Licence.
Item Type: | Working or Discussion Paper (Working Paper) | ||||||
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Subjects: | Q Science > QR Microbiology | ||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Library of Congress Subject Headings (LCSH): | Pathogenic bacteria -- Genome mapping, Genome mapping, Bacterial genomes | ||||||
Journal or Publication Title: | biorxiv | ||||||
Publisher: | Cold Spring Harbour | ||||||
Place of Publication: | BioRxiv | ||||||
Book Title: | GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens | ||||||
Official Date: | 9 November 2017 | ||||||
Dates: |
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Number: | 216788 | ||||||
DOI: | 10.1101/216788 | ||||||
Institution: | University of Warwick | ||||||
Status: | Not Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 7 December 2017 | ||||||
Date of first compliant Open Access: | 7 December 2017 | ||||||
RIOXX Funder/Project Grant: |
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