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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 6.0.1:
New Features and Improvements
  • Primer picking with Primer3
  • Support for NGS error correction and bacterial genome assembly with SparseAssembler
  • Scaffolding of NGS contigs using mate pair information
Bug fixes and Improvements
  • Reduced memory use when importing SAM files
Known Issues
  • Updating contigs in roundtrip more...


  • OS X 10.6.8 or later

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Current Version (6.x)


Downloads 2,702
Version Downloads 10
License Shareware
Date 09 Oct 2015
Platform Intel 64 / OS X / Intel 32
Price $1,440.00
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