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POLYPHRED VERSION 3.5
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POLYPHRED_THUMBPRINT 957890933
TIME 09/05/00 09:48:53
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HELP :
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parameter argument perm. values default
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-ace [Ace file name] none
-d [directory name] ../
-background [background_value] (0.0 - 1.0) 0.25
(or -b)
-ratio (or -r)[ratio_value] (0.0 - 1.0) 0.65
-quality [quality_value] (0 - 50) 30
-group [reg. expression] reg.exp '.+'
-tag [tag type] p or polymorphism genotype
g or genotype
r or rank
-rank [1|2|3|4|5|6] 6-lower rank 3
1-highest rank

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EXAMPLES:
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1. polyphred -ace name.ace -rank 2 > polyphred.output

2. polyphred -ace name.ace -tag g > polyphred.output

3. polyphred -d ~/ace -ace ACE.fasta.ace -tag genotype > polyphred_output

4. polyphred -d ~/ace -ace ACE.fasta.ace -group ".[sr]."
> polyphred_output

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