MEGA provides two convenient methods for aligning coding sequences based on the alignment of protein sequences. In order to accomplish this using the first method, you use the Alignment Explorer to load a data file containing protein-coding sequences. If you click on the Translated Protein Sequences tab you will see that the protein-coding sequences are automatically translated into their respective protein sequence. With this tab active select the Alignment|Align by ClustalW menu item or click on the W tool bar icon to begin the alignment of the translated protein sequences. Once the alignment of the translated protein sequences completes, click on the DNA Sequences tab and youll find that Alignment Explorer automatically aligned the protein-coding sequences according to the aligned translated protein sequences. Any manual adjustments made to the translated protein sequence alignment will also be reflected in the protein-coding sequence tab.
Using the second method, select the Alignment|Align by ClustalW (Codons) menu item after loading the sequence data in Alignment Explorer. Optionally, if MEGA detects that active sequence data may be protein-coding, clicking the W tool bar icon will display a drop down menu for selecting either a DNA or Coding alignment.