Evergreen Online
A forest of constantly updated phylogenetic trees with publicly available whole-genome sequencing data from foodborne, bacterial isolates that were deposited in the short sequencing read archives (NCBI SRA/ENA).
If an isolate is within a threshold of 10 SNPs to a "cluster representative", it won't be used in the phylogenetic tree inference, but will be placed, after the tree is made, onto the same clade as its representative, and marked with an asterisk (*).
Click the buttons to show results or use the search below.
Visualisation is done with Phylocanvas.
Changes in clusters and links to these subtrees:
List of all trees in the system:
). Search for an isolate by its SRA run id (ie. SRR6457909) or for a cluster the isolate might be in:
REFERENCES
- Phylocanvas by the Centre for Genomic Pathogen Surveillance
- Microreact by the Centre for Genomic Pathogen Surveillance
Argimón S, Abudahab K, Goater R, Fedosejev A, Bhai J, Glasner C, Feil E, Holden M, Yeats C, Grundmann H, Spratt B, Aanensen D. 30/11/2016. M Gen 2(11): doi:10.1099/mgen.0.000093
INSTALLATION
Code for running the pipeline on own data is available at bitbucket.
CITATIONS
For publication of results, please cite:
J. Szarvas, J. Ahrenfeldt, J. L. B. Cisneros, M. C. F. Thomsen, F. M. Aarestrup, and O. LundLarge scale automated phylogenomic analysis of bacterial isolates and the Evergreen Online platform
Commun. Biol., vol. 3, no. 1, p. 137, 2020.
FEEDBACK AND COMMENTS
Judit Szarvas ([email protected])
DisclaimerTemplate names are derived from the definition field of RefSeq records, thus Center for Genomic Epidemiology assumes no responsibility for the accuracy of the information presented therein.
Country boundaries/designations do not represent the opinion of the Center for Genomic Epidemiology concerning the legal status of any country, territory, city, or area of its authorities, or concerning the delimitation of its frontiers or boundaries.