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Genome Res. 2018 Sep;28(9):1395-1404. doi: 10.1101/gr.232397.117. Epub 2018 Jul 26.

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

Author information

1
Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom.
2
Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), 1000-029 Lisboa, Portugal.
3
ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, 1959-007 Lisboa, Portugal.
4
Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.
5
Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-004 Lisboa, Portugal.

Abstract

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.

PMID:
30049790
PMCID:
PMC6120633
DOI:
10.1101/gr.232397.117
[Indexed for MEDLINE]
Free PMC Article

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