CodonCode Aligner 11.0.2 Downloads

First time users automatically receive a fully functional free 30-day trial.

After 30 days, the program converts to the demo version. The demo version is a fully functional trace viewer and editor. You can view and print traces, edit traces, and save projects, as long as your projects contain only unassembled samples. The demo version also lets you open existing Aligner projects, and try out many functions, but not to save or print if your project contain contigs.

Updating to CodonCode Aligner 11.0.2

To update older versions to version 11.0.2, please follow the instructions below. If you are upgrading from CodonCode Aligner version 10 or older, please note that you will need a new license key after upgrading, and that this may not be a free upgrade for you.

Updating to CodonCode Aligner 11.0.2 on Windows

  • Navigate to the folder where CodonCode Aligner is installed (usually in a folder called "CodonCode Aligner" in "C:\Program Files\")
  • Double-click the "Check for updates" icon
  • Follow the instructions on the screen to download and install the update to the newest version
    Note: This may not work for users of version 10.0.1. If nothing happens after double-clicking on the "Check for updates" icon, download and use the installer from the link above.

Updating to CodonCode Aligner 11.0.2 on Mac OS X (10.10 and newer)

  • Quit CodonCode Aligner if Aligner is running.
  • Download the installer for CodonCode Aligner 11.0.2 using the links above
  • Install the new version at the same location as the previous version (typically in /Applications).

Please note that updating CodonCode Aligner to the current version will reset the memory available to CodonCode Aligner to the default value. If you had previously changed the memory available to Aligner (for example because your projects are large), you will need to do so again.

Other downloads

Installers for the License Server for CodonCode Aligner are available from the License Server page.

Installers in .msi format are not available anymore, since the .msi format does not support installers for both 32-bit and 64-bit Windows.

For installers of older versions, please contact CodonCode Corporation.


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