PAL2NAL

What is PAL2NAL? What's new Reference Run PAL2NAL Download Contact


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 (dS) and non-synonymous (dN) substitution rates.

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

What's new

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Reference

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If you use PAL2NAL, please cite the following paper:


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)

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 dS and dN:
      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@bioreg.kyushu-u.ac.jp).

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Last modification: 13 May 2013