prodigal(1) microbial (bacterial and archaeal) gene finding program

SYNOPSIS

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]

DESCRIPTION

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.

OPTIONS

-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.