.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.2.
.TH PRODIGAL "1" "September 2014" "prodigal 2.6.1" "User Commands"
.SH NAME
prodigal \- microbial (bacterial and archaeal) gene finding program
.SH SYNOPSIS
.B prodigal
[\fI\,-a trans_file\/\fR] [\fI\,-c\/\fR] [\fI\,-d nuc_file\/\fR] [\fI\,-f output_type\/\fR]
[\-g tr_table] [\-h] [\-i input_file] [\-m] [\-n] [\-o output_file]
[\-p mode] [\-q] [\-s start_file] [\-t training_file] [\-v]
.SH 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.
.SH OPTIONS
.TP
\fB\-a\fR:
Write protein translations to the selected file.
.TP
\fB\-c\fR:
Closed ends.  Do not allow genes to run off edges.
.TP
\fB\-d\fR:
Write nucleotide sequences of genes to the selected file.
.TP
\fB\-f\fR:
Select output format (gbk, gff, or sco).  Default is gbk.
.TP
\fB\-g\fR:
Specify a translation table to use (default 11).
.TP
\fB\-h\fR:
Print help menu and exit.
.TP
\fB\-i\fR:
Specify input file (default reads from stdin).
.TP
\fB\-m\fR:
Treat runs of n's as masked sequence and do not build genes across
them.
.TP
\fB\-n\fR:
Bypass the Shine\-Dalgarno trainer and force the program to scan
for motifs.
.TP
\fB\-o\fR:
Specify output file (default writes to stdout).
.TP
\fB\-p\fR:
Select procedure (single or meta).  Default is single.
.TP
\fB\-q\fR:
Run quietly (suppress normal stderr output).
.TP
\fB\-s\fR:
Write all potential genes (with scores) to the selected file.
.TP
\fB\-t\fR:
Write a training file (if none exists); otherwise, read and use
the specified training file.
.TP
\fB\-v\fR:
Print version number and exit.