Codon Alignment

Purpose: This tool takes nucleotide alignment and returns codon alignment and translates to protein sequences.

How to use: A nucleotide alignment is accepted. The program will automatically identify any standard format. The first sequence in the file will be taken as the master sequence and it should contain no frameshifts. You can select an option to codon-align the alignment starting in different frames or in all three frames. A compensating mutation is within 5 codons (default) of an initial frameshift so that the shifted reading frame is left intact.

• Gene Cutter: a general-purpose alignment method for codon-aligning sets of related unaligned sequences and protein extraction