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maskfasta command
 
Masks sequences in a FASTA file. The ‑qmask masking option is used to specify the desired method. The ‑output option species the filename for the masked sequences. By default, soft masking is used (lower-case). The ‑hardmask option can be used to specify hard masking (Xs or Ns).

Example

usearch -maskfasta proteins.fasta -output masked.fasta -qmask seg