Four sim4 related utilities:

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filterPolishes.c
  Filters polishes by percent identity and composite.  Writes output to
  stdout or a file, takes input from stdin.

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mergePolishes.C
  Merges multiple sim4db outputs.  The output must be from the
  same genomic file, with different cDNA files.

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pickBestPolish.c
  Picks the best polish.  Input is stdin, output is stdout.  No options.

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sortPolishes.c
  Sorts polishes by ESTid or GENid.  Input is stdin, output is stdout.
  Takes "-n N" to set the maximum number of polishes in the input.

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stripPolishes.c
  Removes deflines and alignments from a polish file.