GrapeTree specifications


Unique identifier OMICS_23751
Name GrapeTree
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output format JSON,NWK,SVD
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Javascript, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.5.0
Stability Stable
click, decorator, DendroPy, Flask, itsdangerous, Jinja2, MarkupSafe, networkx, numpy, psutil, Werkzeug
Maintained Yes



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  • person_outline Zhemin Zhou <>
  • person_outline Martin Sergeant <>

Additional information

Publication for GrapeTree

GrapeTree in publications

PMCID: 5886390
PMID: 29621240
DOI: 10.1371/journal.pgen.1007261

[…] now is that it approaches core snp typing in sensitivity. hence, we also recommend investigating the utility of cgmlst rather than snp typing for tracking outbreaks., we note that the graphic tool grapetree () was designed to allow the depiction of relationships based on character data such as mlst from up to 100,000 genomes [] and visualise the cgmlst genetic distances from all of the current […]

PMCID: 5862492
PMID: 29561903
DOI: 10.1371/journal.pone.0194481

[…] other african isolates using multi locus sequence type (mlst) allelic profiles available from the pubmlst database [] (accessed in january 2017). minimum spanning trees generated and visualised in grapetree [] were used to assess the phylogenetic relatedness amongst african isolates; trees were built separately for c. jejuni () and c. coli () isolates. sts represented by botswanan isolates […]

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GrapeTree institution(s)
Warwick Medical School, University of Warwick, Coventry, UK; Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal; Universidade de Lisboa, Faculdade de Medicina, Instituto de Microbiologia and Instituto de Medicina Molecular, Lisboa, Portugal; Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
GrapeTree funding source(s)
Supported by grant from the Wellcome Trust (202792/Z/16/Z) and (BBSRC BB/L020319/1) for the EnteroBase project.

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