CodonCode Aligner is a leading software program for DNA sequence analysis. Widely used in evolution research, biogeography, and other biomedical fields, it offers many features not found in competing programs, including the ability to compare contigs with ClustalW and muscle, trace sharpening, roundtrip editing, and base calling with PHRED, as well as standard features like assembly, trace and contig editing, end clipping, and mutation detection. The download is a demo version where most features except saving and exporting are fully functional. First-time users automatically get a 30-day trial period where all features are fully functional.