Thanks for your query. In fact I have come across a good research paper on genetics where the authors have changed one synonymous codon with another at a particular position i.e. they want to keep the same amino acid sequence in the polypeptide chain but have generated the Maximal Entropy Distribution from a set of sequences obtained by reshuffling the primary coding sequence. These sequences have been used to find the motifs in coding sequence of genes. To generate those set of sequences, I need to take help of a perl script. Actually there will be 20 major groups (i.e. 20 amino acids) and each group will have synonymous number of codons (except methionine & tryptophan). The authors have indicated that this kind of genetic study might be useful in improving the HIV vaccine. That is why I am interested to generate the set of sequences and learn it for the benefit of the students of our department. This is just out of my curiosity.
Harlan Robins,Michael Krasnitz and Arnold J Levine. 2008. The Computational Detection of Functional Nucleotide Sequence Motifs in the Coding Regions of Organisms. Experimental Biology & Medicine 233:665-673. (Open Access)