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bioRxiv · 10.1101/216788

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

Zhou, Z.·Alikhan, N.-F.·Sergeant, M. J.·Luhmann, N.·Vaz, C.·Francisco, A. P.·Carrico, J. A.·Achtman, M.
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Abstract

O_LICurrent methods struggle to reconstruct and visualise the genomic relationships of [≥]100,000 bacterial genomes.\nC_LIO_LIGrapeTree facilitates the analyses of allelic profiles from 10,000s of core genomes within a web browser window.\nC_LIO_LIGrapeTree 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.\nC_LIO_LIGrapeTree 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.\nC_LIO_LIThe GrapeTree package was released under the GPL v3.0 Licence.\nC_LI

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Zhou, Z., Alikhan, N.-F., Sergeant, M. J., Luhmann, N., Vaz, C., Francisco, A. P., Carrico, J. A., Achtman, M.. 2017-11-09. GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens. https://doi.org/10.1101/216788

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