GrapeTree: Visualization of genomic relationships

This plugin generates a minimum-spanning tree and visualizes within GrapeTree:

GrapeTree is developed by: Zhemin Zhou (1), Nabil-Fareed Alikhan (1), Martin J. Sergeant (1), Nina Luhmann (1), Cátia Vaz (2,5), Alexandre P. Francisco (2,4), João André Carriço (3) and Mark Achtman (1)

1. Warwick Medical School, University of Warwick, UK
2. Instituto de Engenharia de Sistemas e Computadores: Investigação e Desenvolvimento (INESC-ID), Lisboa, Portugal
3. Universidade de Lisboa, Faculdade de Medicina, Instituto de Microbiologia and Instituto de Medicina Molecular, Lisboa, Portugal
4. Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
5. ADEETC, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal

Publication: Zhou at al. (2018) GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 28:1395-1404.

Selecting 'All loci' will produce an artefactual analysis because this database contains different kinds of loci that are not equivalent (complete genes, MLST fragments, peptide variable regions, intergenic regions etc.). You are advised to select one of the recommended schemes.

This tool will generate minimum spanning trees trees from allelic profiles. Please check the loci that you would like to include. Alternatively select one or more schemes to include all loci that are members of the scheme.

Analysis is limited to 50,000 records.