---
name: "prodigal"
section: "1"
platform: "linux"
package: "prodigal"
version: "1:2.6.3-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/prodigal"
---

# prodigal(1)

microbial (bacterial and archaeal) gene finding program

## 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.