Output files for search and clustering commands
Hit selection options
The accept and
termination options determine how many
hits USEARCH will store internally before stopping the search for a given query
sequence. Hit selection options determine which of the accepted hits will be
written to the output files. See also weak hits.
Hits are reported in order of decreasing identity (global) or decreasing
alignment score (local).
Most output files report hits, i.e. query-target alignments that meet the
accept criteria. Any number of output files
may be specified, enabling several different types of output to be generated
from one run.