This plugin creates the required input files for ReporTree and runs the tool to identify and characterize genetic clusters.

ReporTree is developed by: Verónica Mixão (1), Miguel Pinto (1), Daniel Sobral (1), Adriano Di Pasquale (2), João Paulo Gomes (1), and Vítor Borges (1)

  1. Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
  2. National Reference Centre (NRC) for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale Dell'Abruzzo E del Molise "Giuseppe Caporale" (IZSAM), Teramo, Italy.

Publication: Mixão at al. (2023) ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data Genome Med 15:43.

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

Analysis is limited to 10,000 records.

Include fields

Select fields to include in ReporTree metadata.

  • Cluster date field:

  • Partitions: