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CASSIOPEE(1) User Commands CASSIOPEE(1)

NAME

Cassiopee - manual page for Cassiopee Version 1.0

DESCRIPTION

Usage:

-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

SEE ALSO

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.
April 2014 Cassiopee Version 1.0