PAL2NAL

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What is PAL2NAL?

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PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) substitution rates.

If the input is a pair of sequences, PAL2NAL automatically calculates d_S and d_N by the codeml program in PAML.

What's new

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Dec 02, 2011: Updated to version 14.
- Codon tables are expanded. (Now all the codon tables in NCBI are covered.)
Jul 26, 2010: The script in the distribution version is updated to v13.
Sep 08, 2009: If d_S and d_N are calculated, the numbers of synonymous (S) and non-synonymous (N) sites are also reported.
Apr 03, 2009: New mirror site for PAL2NAL at Kyoto University.
Feb 05, 2007: Updated to version 12.
- If you use the same IDs in the input files 1 and 2, then the order of the sequences does not have to be the same.
- Some routines in the script is optimized, and now it is faster than before.
- In case of the error ("inconsistency between pep and nuc"), the script automatically runs bl2seq to show why the protein seq and DNA seq don't match.

Reference

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If you use PAL2NAL, please cite the following paper:

Mikita Suyama, David Torrents, and Peer Bork (2006)
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Nucleic Acids Res. 34, W609-W612.

Run PAL2NAL (try with an example)

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INPUT FILE 1

Put your multiple sequence alignment of proteins (either in CLUSTAL or in FASTA format)

The server automatically detects the file format.
In the CLUSTAL format, you can select some specific positions by '#' under the alignment; see the example.
How to specify stop codons and frame shifts in the alignment..

or

upload

INPUT FILE 2

Put your DNA (or mRNA) sequences (in FASTA format)

or

upload

Option setting

Codon table:
Universal code (NCBI: transl_table=1)
Vertebrate mitochondrial code (NCBI: transl_table=2)
Yeast mitochondrial code (NCBI: transl_table=3)
Mold, Protozoan, and Coelenterate Mitochondrial code and Mycoplasma/Spiroplasma code (NCBI: transl_table=4)
Invertebrate mitochondrial code (NCBI: transl_table=5)
Ciliate, Dasycladacean and Hexamita nuclear code (NCBI: transl_table=6)
Echinoderm and Flatworm mitochondrial code (NCBI: transl_table=9)
Euplotid nuclear code (NCBI: transl_table=10)
Bacterial, archaeal and plant plastid code (NCBI: transl_table=11)
Alternative yeast nuclear code (NCBI: transl_table=12)
Ascidian mitochondrial code (NCBI: transl_table=13)
Alternative flatworm mitochondrial code (NCBI: transl_table=14)
Blepharisma nuclear code
Chlorophycean mitochondrial code
Trematode mitochondrial code
Scenedesmus obliquus mitochondrial code
Thraustochytrium mitochondrial code
Remove gaps, inframe stop codons:
No
Yes
- Calculate d_S and d_N:
  No
  Yes (valid only if the input is a pair of sequences)
Remove mismatches: (mismatched codons between protein and DNA)
No
Yes
Use only selected positions ('#' under the input alignment):
No
Yes
Output format:
CLUSTAL PAML FASTA Codon with Amino acid

Download

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The distribution version of PAL2NAL is also available.
Current version: v14 (2 December 2011) [download].

Contact

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For comments and questions, send a message to Mikita Suyama (mikita@genome.med.kyoto-u.ac.jp).

Last modification: 2 December 2011