I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database, but that option is excluded for remote searches. Should I use a script to filter the search results, like -gilist, or is there an easier way?
I would also like to know this, but for local blast vs nr!