Sometimes it useful to perform a nucleotide protein coding gene sequence alignment based on codons, not on individual nucleotides. For example for further codon model analysis it is important to have full codons.
The problem here is that you are discarding part of the information which could be potentially used for the sequence alignment. E.g. if you have slowly evolving low-complexity region adjacent to a quickly evolving one, the amino acid induced alignment could be wrong, while incorporating nucleotide sequence potentially allows to make the alignment more accurate.
Can you recommend any software for multiple codon sequence alignment? Preferably available for offline use.