Compressed amino acid alphabets are supported for all search and clustering commands that use indexes (see index options). The alphabet can be specified using the -alpha option. The alphabet is specified as a string containing every letter in the standard 20-letter amino acid alphabet exactly once. Groups of letters that are to be represented by a single symbol in the reduced alphabet are separated by commas.
The order the groups are specified is not significant. By convention, the group is represented by its first letter, so for example in the above alphabet the 4-mer MARW would be compressed to IAKF.
By default, protein ublast is the only command that uses compressed alphabets. This is because other commands are generally used for high-identity search and clustering tasks where compressed alphabets typically give only a marginal improvement in sensitivity.
-alpha A,KR,DENQ,C,G,H,ILVM,FYW,P,ST -pattern 10111011