-u: save index for later use -s: sequence to index -p: pattern to search -f: file containing pattern to search -o: output file -r: apply tree reduction -m: search mode: 0=DNA, 1=RNA, 2=Protein -a: allow alphabet ambiguity search -n: max consecutive N allowed matches in search -e: max substitution allowed matches in search -i: max indel allowed matches in search -g: generates a dot file of the graph -d: max depth of the graph -t: output format: 0:tsv (default), 1:json -x: minimum position in sequence -y: maximum position in sequence -v: show version -h: show this message

RELATED TO cassiopee…

The full documentation for Cassiopee is maintained as a Texinfo manual. If the info and Cassiopee programs are properly installed at your site, the command

  • info Cassiopee

should give you access to the complete manual.