cd-hit-est-2d(1) on Linux
The text 39bd05a6984e, as Debian 9 (Stretch) shipped it.
run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format
Flags it lists
-
-A -
-AL -
-AS -
-B -
-G -
-M -
-S -
-S2 -
-T -
-U -
-aL -
-aS -
-b -
-c -
-d -
-g -
-gap-ext -
-h -
-i -
-i2 -
-l -
-mask -
-match -
-mismatch -
-n -
-o -
-p -
-r -
-s -
-s2 -
-uL -
-uS