Man page - prodigal(1)

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Package: prodigal
apt-get install prodigal

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prodigal(1)

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prodigal

Manual

PRODIGAL

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

NAME

prodigal - 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.