cd-hit-est(1) on Linux
The text 20cee81c547d, as Debian 11 (Bullseye) shipped it.
run CD-HIT algorithm on RNA/DNA sequences
Flags it lists
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-A -
-AL -
-AS -
-B -
-G -
-M -
-P -
-S -
-T -
-U -
-aL -
-aS -
-ap -
-b -
-c -
-cx -
-cy -
-d -
-g -
-gap-ext -
-h -
-i -
-j -
-l -
-mask -
-match -
-mismatch -
-n -
-o -
-op -
-p -
-r -
-s -
-sc -
-sf -
-uL -
-uS