---
name: "pal2nal.pl"
section: "1"
platform: "linux"
package: "pal2nal"
version: "14.1-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pal2nal.pl"
---

# pal2nal.pl(1)

use insight from protein alignment for nucleotide alignment

## NAME

pal2nal.pl - use insight from protein alignment for nucleotide alignment

## SYNOPSIS

**pal2nal.pl** *pep.aln  nuc.fasta*  \[*nuc.fasta*...\]  \[*options*\]

## DESCRIPTION

pal2nal.pl  (v13)

- pep.aln:

  protein alignment either in CLUSTAL or FASTA format

- nuc.fasta:

  DNA sequences (single multi-fasta or separated files)

- Options:

  **-h**            Show help

-

  **-output** (clustal\|paml\|fasta\|codon)

-

  Output format; default = clustal

- **-blockonly**

  Show only user specified blocks '#' under CLUSTAL alignment (see example)

- **-nogap**

  remove columns with gaps and inframe stop codons

- **-nomismatch**

  remove mismatched codons (mismatch between pep and cDNA) from the output

-

  **-codontable** (universal\|vmitochondria)

-

  Codon table

-

  \- universal (default) - vmitochondria -\> vertebrate mitochondrial

- **-html**

  HTML output (only for the web server)

- **-nostderr**

  No STDERR messages (only for the web server)

-

  \- sequence order in pep.aln and nuc.fasta should be the same.

-

  \- IDs in pep.aln are used in the output.

pal2nal.pl  (v13)

Usage:  pal2nal.pl  pep.aln  nuc.fasta  \[nuc.fasta...\]  \[options\]

- pep.aln:

  protein alignment either in CLUSTAL or FASTA format

- nuc.fasta:

  DNA sequences (single multi-fasta or separated files)

- Options:

  **-h**            Show help

-

  **-output** (clustal\|paml\|fasta\|codon)

-

  Output format; default = clustal

- **-blockonly**

  Show only user specified blocks '#' under CLUSTAL alignment (see example)

- **-nogap**

  remove columns with gaps and inframe stop codons

- **-nomismatch**

  remove mismatched codons (mismatch between pep and cDNA) from the output

-

  **-codontable** (universal\|vmitochondria)

-

  Codon table

-

  \- universal (default) - vmitochondria -\> vertebrate mitochondrial

- **-html**

  HTML output (only for the web server)

- **-nostderr**

  No STDERR messages (only for the web server)

-

  \- sequence order in pep.aln and nuc.fasta should be the same.

-

  \- IDs in pep.aln are used in the output.

## SEE ALSO

The full documentation for **pal2nal.pl** is maintained as a Texinfo manual.  If the **info** and **pal2nal.pl** programs are properly installed at your site, the command

-

  **info pal2nal.pl**

should give you access to the complete manual.