From the docs...

55% cd-hit -n 4 -c 0.55 or
mcd-hit -n 3 -c 0.55

When I try

cd-hit
-i ./Scratch/somefile.fa
-o ./Scratch/somefile.fa.55
-c 0.55
-b 20
-M 1400
-n 4
-l 40
-L 0
-d 40
-t 2

I get the following error...

Fatal Error
Too short word length, increase it or the tolerance


Fixed by using


mcd-hit
-i ./Scratch/somefile.fa
-o ./Scratch/somefile.fa.55
-c 0.55
-b 20
-M 1400
-n 3
-l 40
-L 0
-d 40
-t 2


The optimal wordsize choice is emperically determined, it would be nice if we could analytically determine their values.

Maybe even a hybrid word size approach would be optimal.