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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 more...

What's New

Version 6.0.2:
Bug fixes and Improvements
  • Fixed a problem introduced in version 6.0.1
Known Issues
  • Updating contigs in roundtrip editing fails if any of the samples or contigs has unaligned ends; to avoid this problem, use ClustalW to generate the contigs for roundtrip editing
  • Aliases (shortcuts) to files do sometimes not work properly, for example when more...


  • OS X 10.6.8 or later

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Current Version (6.x)


Downloads 2,721
Version Downloads 16
License Shareware
Date 13 Oct 2015
Platform Intel 64 / OS X / Intel 32
Price $1,440.00
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