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hyattpd edited this page Aug 21, 2014 · 5 revisions

Short and Long Options

Prodigal supports both long and short options. These four commands are all equivalent:

$ prodigal -i sequence.fna -o genes.gff -f gff
$ prodigal -isequence.fna -ogenes.gff -fgff
$ prodigal --input_file sequence.fna --output_file genes.gff --output_format gff
$ prodigal --input_file=sequence.fna --output_file=genes.gff --output_format=gff

Prodigal 2.x: Older versions of Prodigal only support short options, and there must be a space between the option and its parameter.

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