Codon Code Aligner sequence assembly and alignment

Sequence Assembly with CodonCode Aligner

CodonCode Aligner is an easy-to-use program for sequence assembly, contig editing, and mutation detection. Features include:

  • Multiple sequence assembly and sequence alignment algorithms
  • Manual and automated sequence editing
  • Align contigs to each other and get back to the underlying trace data with a simple double-click
  • Reference sequences and difference tables
  • Sensitive mutation detection
  • Advanced methods for heterozygous indel analysis
  • Automation tools: assemble by name & scripting

CodonCode Aligner offers many unique features not found in other programs, but is significantly more affordable.


Get A Free Trial

Download the demo version and get a fully functional 30-day trial. No forms to fill out.

CodonCode Aligner free download

Available for Windows and Mac OS X. Demo versions can be upgraded to the full version by entering a purchased license key.

CodonCode Aligner prices and ordering information


What's New

CodonCode Aligner 6.0.1
is now available


New features in 6.0.1:

Primer Design

Bacterial Genome Assembly



Learn More


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