ABSTRACT Motivation: Not only sequence data continues to outpace annotation information, but the problem is further exacerbated when organisms are underrepresented in the annotation databases. This is the case with non human-pathogenic viruses which occur frequently in metagenomic projects. Thus there is a need for tools capable of detecting and classifying viral sequences. Results: We describe VIRALpro a new effective tool for identifying capsid and tail protein sequences, which are the cornerstones toward viral sequence annotation and viral genome classification. Availability: The data, software, and corresponding web server are available from: http://scratch.proteomics.ics.uci.edu as part of the SCRATCH suite.