1. Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
2. Department of Mathematics and Statistics, Helsinki Institute of Information Technology (HIIT), FI-00014 University of Helsinki, Finland
3. Department of Computer Science, Aalto University, FI-00076 Espoo, Finland
4. Present address: Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
5. Present address: Department of Mathematics, University of Oslo, 0316 Oslo, Norway
6. Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
7. Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK