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cassiopee(1)


NAME

   cassiopee - manual page for Cassiopee Version 1.0

SYNOPSIS

   cassiopee [Options] <sequence>

DESCRIPTION

   Usage:
   -l: maximum index depth / maximum pattern size

   -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



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