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Standard (Mandatory) qualifiers (* if not always prompted):
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
-count integer [1] Number of times to perform the mutation
operations (Integer 0 or more)
-point menu [0] Types of point mutations to perform
(Values: 0 (None); 1 (Any of the following);
2 (Insertions); 3 (Deletions); 4 (Changes);
5 (Duplications); 6 (Moves))
-block menu [0] Types of block mutations to perform
(Values: 0 (None); 1 (Any of the following);
2 (Insertions); 3 (Deletions); 4 (Changes);
5 (Duplications); 6 (Moves))
* -codon menu [0] Types of codon mutations to perform.
These are only done if the sequence is
nucleic. (Values: 0 (None); 1 (Any of the
following); 2 (Insertions); 3 (Deletions); 4
(Changes); 5 (Duplications); 6 (Moves))
[-outseq] seqoutall [.] Sequence set(s)
filename and optional format (output USA)

Additional (Optional) qualifiers (* if not always prompted):
* -inframe boolean [N] Do 'codon' and 'block' operations in
frame

Advanced (Unprompted) qualifiers:
-othersequence seqall [asis:N] If you require that the resulting
mutated sequence should not match a set of
other sequences, then you can specify that
set of sequences here. For example, if you
require that the mutated sequence should not
be the same as the input sequence, enter
the input sequence here. If you want the
result to be different to previous results
of this program, specify the previous result
sequences here. The program will check that
the result does not match the sequences
specified here before writing it out. If a
match is found, then the mutation is started
again with a fresh copy of the input
sequence. If, after 10 such retries, there
is still a match to the set of sequence
given here, then the matching mutated
sequence is written with a warning message.
-minimum integer [1] Minimum size for a block mutation
(Integer 0 or more)
-maximum integer [10] Maximum size for a block mutation (Any
integer value)

General qualifiers:
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose