I'm looking for free tools to define genes functions of bacteria (enzymatic functions) and similarities with known genes, I'm not a big fan of BLAST !
thank you in advance
One of the most widely used tools for prokaryotic genome annotation is prokka. It requires only a (meta)genome sequence, and when installed properly on a modern computer (8+ CPUs) it will fully annotate a prokaryotic genome in under 10 minutes. However, it will require additional hidden Markov model databases such as Pfam and TIGRFams, which did not come standard last time I checked.