pair_align(1) on Linux
The text 2994a40bc6e1, as Debian 9 (Stretch) shipped it.
Pairwise alignment SYNOPSIS DESCRIPTION OPTIONS -h, --help --version-check BOOL --version -s, --seq INPUT_FILE -a, --alphabet STRING -m, --method STRING -o, --outfile OUTPUT_FILE -g, --gop INTEGER -e, --gex INTEGER -ma, --matrix STRING -ms, --msc INTEGER -mm, --mmsc INTEGER -lo, --low INTEGER -hi, --high INTEGER -c, --config STRING ALIGNMENT CONFIGURATION VERSION