DNA based alignments - Sun-Yanbo/FasParser GitHub Wiki

If you just want to construct DNA alignments, no metter whether the sequences are coding regions, it is very easy for FasParser. There are three Aligners: Muscle, Mafft, and Prank-DNA, can be used to generate DNA alignments. Muscle is always faster than the other two, while the Prank-DNA is always able to generate more correct results.