pair_align(1) on Linux
The text ae760f5f081f, as Debian 8 (Jessie) shipped it.
Pairwise alignment SYNOPSIS DESCRIPTION -h, --help --version -s, --seq IN.fa -a, --alphabet ALPHABET -m, --method METHOD -o, --outfile OUT -g, --gop INT -e, --gex INT -ma, --matrix MATRIX_FILE -ms, --msc INT -mm, --mmsc INT -lo, --low INT -hi, --high INT -c, --config CONF ALIGNMENT CONFIGURATION VERSION