hhconsensus(1) on Linux
The text 250294be5bb5, as Debian 9 (Stretch) shipped it.
calculate the consensus sequence for an A3M/FASTA input file
Flags it lists
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-M -
-cov -
-i -
-id -
-o -
-oa2m -
-oa3m -
-ofas -
-qid -
-qsc -
-s -
-v