GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
By Zhemin Zhou, Nabil-Fareed Alikhan, M. Sergeant, Nina Luhmann, Cátia Vaz, Alexandre P. Francisco, João André Carriço, Mark Achtman. bioRxiv, 2017
885 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/6c5cbcd41de883e28674ec010743d4774597c239
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In Molecular Biology
- Yulei Fan
- Gerry Tonkin-Hill
- Simon R. Harris
- Nabil-Fareed Alikhan
- John Lees
- Jukka Corander
- Stephen D. Bentley
- Zhemin Zhou
In Plant Science
Citations in the corpus
- The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity (2019, methodology): “HC400_299 was investigated by maximumlikelihood trees of core, nonrepetitive SNPs called against a reference draft genome with the help of the EnteroBase Dendrogram GUI.”
- Fast and flexible bacterial genomic epidemiology with PopPUNK (2018, methodology): “…we selected a range of previously published datasets on ten different bacterial species (Aanensen et al. 2016; Kallonen et al. 2017; Kremer et al. 2017; Koelman et al. 2017; Lees et al. 2016; Grad et al. 2016; Lees et al. 2017; Croucher et al. 2013, 2015; Alikhan et al. 2018; Cohen et al. 2015) .”