maskseq allows you to mask off regions of a sequence with a specified letter. To mask off bases 10 to 12 from a sequence gatta.seq and write to the new sequence file gatta2.seq: % maskseq gatta.seq gatta2.seq -reg=10-12 To mask off bases 20 to 30 from a sequence hdh.seq using the character n and write to the new sequence file hdh2.seq: % maskseq hdh.seq hdh2.seq -reg=20-30 -mask=n To mask off the regions 20 to 23, 34 to 45 and 88 to 90 in yuy.seq: % maskseq yuy.seq yuy2.seq -reg=20-23,34-45,88-90 Mandatory qualifiers:
Optional qualifiers:
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