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
- Dec 02, 2011: Updated to version 14.
- Jul 26, 2010: The script in the distribution version is updated to v13.
- Sep 08, 2009: If dS and dN 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
- 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.
If you use PAL2NAL, please cite the following paper:
The distribution version of PAL2NAL is also available.
Current version: v14 (2 December 2011) [download].
For comments and questions, send a message to Mikita Suyama (firstname.lastname@example.org).
Last modification: 13 May 2013