Blast2go is the gene ontology annotation program for eukaryotes.
Some time after 2012, it became commercialised, although the free usage of early version is still permitted.
Blast2go the program is GUI, but there is a command-line alternative called b2g4pipe.
The best version of b2g4pipe to use is
As this is the one Peter Cock uses for the Galaxy wrapper version 8 in March 2015.