New in CodonCode Aligner Version 2.0

This page describes the most important changes and new features in CodonCode Aligner version 2.0. Features added in CodonCode Aligner version 1.6 on a separate page.

All of these new features have been requested by users - thanks to all who have given us feedback.


  • Restriction maps: Find restriction enzyme cut sites and view restriction maps.
  • Trace sharpening: Get a better look at your data with Aligner's trace sharpening.
  • Print preview: See what's being printed instead of wasting paper, even on Windows.
  • Align to reference by name: Quickly form many contigs by aligning samples to reference sequences.
  • Split heterozygous indels: Split heterozygous indel chromatograms into two new sequences which show the size of your indel.
  • Customizable toolbars: Pick the buttons you need for your work - for each window.
  • Improved mutation finding: Quickly confirm or reject mutations, view confirmed mutations, auto-match low-quality sequences like dye blobs to the consensus, and define regions to ignore.
  • Much more: Change ambiguities to bases, convert low quality bases to N, exclude the reference from the consensus sequence, support for scripting, duplicate samples, delete selected items from trash, find and describe mutations in text sequences, export unphased haplotype sequences, improvements for large reference sequences, ...


Interested? Watch the movie or go to the download page.



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