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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 5.1.5:

Note: Version 5 requires a new license key. Version 5 is a free upgrade for all users with a current update and support agreement as of March 27, 2014. This includes all users who purchased a license within the past 12 months. Users qualifying for a free upgrade will receive a new license key by email. If you have questions about your license key or support agreement, or more...


  • OS X 10.5.8 or later

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Current Version (5.x)


Downloads 2,616
Version Downloads 91
License Demo
Date 03 Feb 2015
Platform Intel 64 / OS X / PPC 32 / Intel 32
Price $1,440.00
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