prodigal - microbial (bacterial and archaeal) gene finding program

       Prodigal  (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal)
       gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.

       prodigal - microbial (bacterial and archaeal) gene finding program

-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 input file (default reads from stdin).

       -m:    Treat runs of n's as masked sequence and do not build genes across them.

       -n:    Bypass the Shine-Dalgarno trainer and force the program to scan for motifs.

       -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.

prodigal 2.6.1                                   September 2014                                      PRODIGAL(1)

prodigal [-atrans_file] [-c] [-dnuc_file] [-foutput_type] [-g tr_table] [-h] [-i input_file] [-m] [-n]
       [-o output_file] [-p mode] [-q] [-s start_file] [-t training_file] [-v]