Funding: Supported by a research Flagship grant from the South African Medical Re-search Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI), a Royal Society Newton Advanced Fellowship (TdO), the VIROGENESIS project receives funding from the European Union’s Horizon 2020 Research and Innovation Programme (under Grant Agreement no. 634650) and the National Institutes of Health Common Fund, grant number U24HG006941. Pieter Libin was supported by a PhD grant of the FWO (Fonds Wetenschappelijk Onderzoek -Vlaanderen). This work was supported by Decit/SCTIE/MoH and CNPq (440685/2016-8 and 440856/2016-7); by CAPES (88887.130716/2016-00, 88881.130825/2016-00 and 88887.130823/2016-00); and by EU’s Horizon 2020 Programme through ZIKAlliance (PRES-005-FEX-17-4-2-33). Ana Abecasis was supported by Fundação para a Ciência e Tecnologia (FCT) through funds to GHTM-UID/Multi/04413/2013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: Dr. Koen Deforche is one of the owners of the commercial company, EMWEB.In recent years, an increasing number of outbreaks of Dengue, Chikungunya and Zika viruses have been reported in Asia and the Americas. Monitoring virus genotype diversity is crucial to understand the emergence and spread of outbreaks, both aspects that are vital to develop effective prevention and treatment strategies. Hence, we developed an efficient method to classify virus sequences with respect to their species and sub-species (i.e. serotype and/or genotype). This tool provides an easy-to-use software implementation of this new method and was validated on a large dataset assessing the classification performance with respect to whole-genome sequences and partial-genome sequences. Available online: http://krisp.org.za/tools.php.