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Prodigal for R, for gene prediction.
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PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.
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Usage: prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
[-g tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file]
[-p mode] [-q] [-s start_file] [-t training_file] [-v]
-a: Write protein translations to the selected file.
-c: Closed ends. Do not allow genes to run off edges.
-d: Write nucleotide sequences of genes to the selected file.
-f: Select output format (gbk, gff, or sco). Default is gbk.
-g: Specify a translation table to use (default 11).
-h: Print help menu and exit.
-i: Specify FASTA/Genbank input file (default reads from stdin).
-m: Treat runs of N as masked sequence; don't build genes across them.
-n: Bypass Shine-Dalgarno trainer and force a full motif scan.
-o: Specify output file (default writes to stdout).
-p: Select procedure (single or meta). Default is single.
-q: Run quietly (suppress normal stderr output).
-s: Write all potential genes (with scores) to the selected file.
-t: Write a training file (if none exists); otherwise, read and use
the specified training file.
-v: Print version number and exit.