Covidex

Viral subtypes or clades represent clusters among isolates from the global population of a defined species. Subtypification is relevant for studies on virus epidemiology, evolution and pathogenesis. In this sense, Covidex was developed as an open source alignment-free machine learning subtyping tool. It is a shiny app that allows fast and accurate classification of viral genomes in pre-defined clusters. If more than 1000 sequences are loaded the tool will run in multithread mode. Capable of classifying 16000 genome sequences in less than a minute (AMD Ryzen 7 1700 8-core Processor 3 GHz)
For a Web-based version of the app (only for small datasets: 100 seqs max) please go to
http://covidex.unlu.edu.ar
If you use Covidex please consider citing the following preprint:
https://biorxiv.org/cgi/content/short/2020.08.21.261347v1
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