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

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...

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Detalles Bibliográficos
Autores principales: Zhou, Zhemin, Alikhan, Nabil-Fareed, Sergeant, Martin J., Luhmann, Nina, Vaz, Cátia, Francisco, Alexandre P., Carriço, João André, Achtman, Mark
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120633/
https://www.ncbi.nlm.nih.gov/pubmed/30049790
http://dx.doi.org/10.1101/gr.232397.117
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author Zhou, Zhemin
Alikhan, Nabil-Fareed
Sergeant, Martin J.
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre P.
Carriço, João André
Achtman, Mark
author_facet Zhou, Zhemin
Alikhan, Nabil-Fareed
Sergeant, Martin J.
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre P.
Carriço, João André
Achtman, Mark
author_sort Zhou, Zhemin
collection PubMed
description 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.
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spelling pubmed-61206332018-09-05 GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens Zhou, Zhemin Alikhan, Nabil-Fareed Sergeant, Martin J. Luhmann, Nina Vaz, Cátia Francisco, Alexandre P. Carriço, João André Achtman, Mark Genome Res Method 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. Cold Spring Harbor Laboratory Press 2018-09 /pmc/articles/PMC6120633/ /pubmed/30049790 http://dx.doi.org/10.1101/gr.232397.117 Text en © 2018 Zhou et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ 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/.
spellingShingle Method
Zhou, Zhemin
Alikhan, Nabil-Fareed
Sergeant, Martin J.
Luhmann, Nina
Vaz, Cátia
Francisco, Alexandre P.
Carriço, João André
Achtman, Mark
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_full GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_fullStr GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_full_unstemmed GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_short GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
title_sort grapetree: visualization of core genomic relationships among 100,000 bacterial pathogens
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120633/
https://www.ncbi.nlm.nih.gov/pubmed/30049790
http://dx.doi.org/10.1101/gr.232397.117
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