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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, Cátia, Francisco, Alexandre P. , Carriço, João André and Achtman, Mark (2018) GrapeTree : visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research, 28 (10). pp. 1395-1404. doi:10.1101/gr.232397.117 ISSN 1088-9051.
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Official URL: http://doi.org/10.1101/gr.232397.117
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 which 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.
| Item Type: | Journal Article | ||||||||||||
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| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||||||||||
| Library of Congress Subject Headings (LCSH): | Pathogenic bacteria -- Functional genomics, Bacterial genomes, Algorithms | ||||||||||||
| Journal or Publication Title: | Genome Research | ||||||||||||
| Publisher: | Cold Spring Harbor Lab Press | ||||||||||||
| ISSN: | 1088-9051 | ||||||||||||
| Official Date: | October 2018 | ||||||||||||
| Dates: |
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| Volume: | 28 | ||||||||||||
| Number: | 10 | ||||||||||||
| Page Range: | pp. 1395-1404 | ||||||||||||
| DOI: | 10.1101/gr.232397.117 | ||||||||||||
| Status: | Peer Reviewed | ||||||||||||
| Publication Status: | Published | ||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||
| Date of first compliant deposit: | 26 July 2018 | ||||||||||||
| Date of first compliant Open Access: | 26 July 2018 | ||||||||||||
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| Is Part Of: | EnteroBase (BBSRC BB/L020319/1) was developed by N-F.A., M.J.S. and Z.Z. (equal contributions) under guidance by M.A. Additional grant support was from the Wellcome Trust (202792/Z/16/Z). AF, CV and JAC were partially funded by BacGenTrack (TUBITAK/0004/2014; FCT/Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Ara srrma Kurumu, Tübitak)). | ||||||||||||
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