| Specifies that only top hits should be written to the output files. A top hit has the best identity (if the -id option is specified) or the best expectation value (if -evalue is specified). If two ore more hits have the best value, then they are all output. Note that the default value of -maxaccepts is 1 for commands based on the USEARCH algorithm, which means that at most one hit will be found and the -top_hits_only option therefore has no effect unless -maxaccepts is set to a value > 1. |