I have a little example fasta file with protein fragments to figure out how usearch works:
>seq1 TKEHALSKERAA >seq2 KKEHALSKERAR >seq3 AAHAASAERAAE >seq4 AAHAASAERAAS
I used usearch with the following options:
usearch -cluster_fast ex.fasta -id 0.5 -uc cluster.uc
I expect at most 2 clusters (1,2) and (3,4) but the result contains only singletons.I decreased the identity and also the gap penalties but the result is the same.