Download CodonCode Aligner

Download the latest version of CodonCode Aligner for macOS or Windows. Trial use and paid licenses share the same installer — no key is needed to try the software.

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Trials for CodonCode Aligner

First time users automatically receive a free fully functional 30-day trial - no forms to fill out.

After 30 days, the program converts to the demo version. The demo version still allows you to open projects, import files, view and edit Sanger chromatograms, and try some of CodonCode Aligners functions, but saving, printing, and advanced functions are disabled.

Updating to CodonCode Aligner 12.0.4

To update older versions to version 12.0.4, please follow the instructions below. If you are upgrading from CodonCode Aligner version 11 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 12.0.4 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 12.0.4 on Mac OS X (10.10 and newer)

Quit CodonCode Aligner if Aligner is running.
Download the installer for CodonCode Aligner 12.0.4 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.

System Requirements

macOS 10.10 or later
Windows 7, 8, 10, or 11

Other downloads

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

Windows users who cannot download .exe files can download a ZIP archive that contains the installer for Windows: Preparing your download link..

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.

Frequently Asked Questions

Q: Do I need a license key to start the free trial?

A: No, you do not need a license key for the initial 30-day trial. New users automatically get a fully functional 30-day trial so they can evaluate if CodonCode Aligner meets their needs. If you decide to purchase after trying, you will receive a license key that will unlock all features permanently.

Q: How long does the free trial last?

A: The free trial is valid for 30 days.

Q: What happens after the trial period ends?

A: After 30 days, the software reverts to demo mode, and saving, printing, and other functions are disabled. If you decide to purchase a license, you will receive a license key that you can enter to unlock all features permanently.

Q: Are there any differences between the trial and the full version?

A: The trial version and the full version have exactly the same functionality. The only difference is that the trial version expires after 30 days and reverts to demo mode, while the full (purchased) version does not expire.

Q: Are purchased licenses permanent, or is there an annual subscription?

A: CodonCode Aligner licenses are permanent and do not require an annual subscriptions. However, new versions of operating systems introduced afterwards sometimes make changes that make old versions unusable. We offer paid annual extensions of the initial 12 months update and support period, but these are optional, not required.

Q: How do I update to a newer version of CodonCode Aligner?

A: When new versions are released, we send emails to customers announcing the release, and include new license keys for major upgrades for customers with a current update and support agreement (the initial purchase includes 12 months of free upgrades and support). Detailed instructions on how to update are given above.

Q: Is internet access required to use the software?

A: In general, internet access is not required. Only a few functions, for example starting Blast searches, retrieving sequences from Genbank, or checking for updates, require an internet connection.

Q: Where can I find older versions?

A: For installers of older versions, please contact CodonCode Corporation.

Q: Where can I get help?

A: CodonCode Aligner comes with extensive help documentation that is available through the Help menu in CodonCode Aligner, and as a PDF file in the folder where the program is installed. A number of video tutorials is also available.
If you cannot find the information you are looking for, please contact us.