You can limit your Standalone BLAST+ software by organism or taxonomic group if you use the list of GI numbers or accession numbers that corresponds to all of the sequence records for an organism or a taxonomic group in the database.

To obtain the unique identifier list, search the sequence database that you want with the name of your organism or taxonomic group either on the web or through NCBI's APIs. The identifier list needs to be saved as a text file, one identifier per line. (BLAST will ignore identifiers that do not belong to the database.)

The BLAST+ binaries use the -gilist or -seqids parameters to incorporate the identifier list into the search:

blastn –db –query in.fas –gilist rodent.gil –out output.txt
blastp –db –query in.fas –seqids mammals.acc –out output.txt