reCOGnizer performs domain based annotation with RPS-BLAST, using Hidden Markov Models (HMM) from COG database. It rebuilds COG database for multithreaded annotation, organizes information regarding COG IDs and respective categories, obtains EC numbers using resources from the eggNOG database and organizes all this information into TSV and EXCEL files for easy handling by users or pipelines. It also produces a Krona plot representing the quantification of COG functions identified.