Develop tools

IT tools

The COMPARE working space enables easy sharing of sequence data and metadata between collaborators in an ordered database. In addition to providing a platform for collaboration, the working space also simplifies upload of sequence data to the European Nucleotide Archive (ENA), and offers a few basic analyses such as species prediction, MLST typing, and prediction of acquired resistance. The platform is undergoing continuous improvements and the addition of more analyses methods has been planned.

The Center for Genomic Epidemiology is continuously developing user friendly web-tools for analysis of sequence data. These tools include species prediction (KmerFinder), phenotyping (ResFinder, VirulenceFinder, etc.), typing (MLST, SeroTypeFinder etc.), and inference of phylogenies (CSIPhylogeny (SNP), NDtree (Nucleotide Difference)).

Several of these tools have been combined in to a single workflow, the Bacterial Analysis Pipeline.

All of the tools are developed in the spirit of open science and all data uploaded to any of the services should be intended for the public domain at some point. All data are kept confidential, but the services are only intended for data that are destined for the public domain.

The complete list of available services can be found here.

The COMPARE project has supported efforts to further improve and consolidate these tools and services.


Jeffrey Skiby
Project Manager
Technical University of Denmark
+45 35 88 66 04, Mobile +45 22 84 45 27


Ole Lund
Technical University of Denmark