Codon Align is not an alignment program per se . Instead it uses an existing alignment of proteins to introduce triplet gaps into the coding sequences wherever gaps occur in the aligned proteins. The result in an alignment of coding regions in which codon integrity is preserved . What you need Each package includes the CodonAlign program, documentation in PDF format, example input files, and a C source code file.
Alignment programs introduce gaps into sequences to maximize identities across sites.
The biological interpretation of gaps is that they represent insertion or deletion mutations that occurred during the divergence of those sequences. When gaps occur within codons those mutations would have been frameshift mutations that would have rendered the proteins non-functional. A more reasonable interpretation is that insertion and deletion mutations that survived to become fixed into populations maintained reading frames, and that the frameshifting gaps in DNA alignments are artifactual results of the alignment algorithms. There are a variety of phylogenetic analyses that involve taking codons into account. Those analyses either discard from the analysis codons in which one of the taxa includes a gap, or they treat gaps within codons as unknown information.