CodonCode Aligner Downloads

From this page, you can download installers for CodonCode Aligner.

When you are using CodonCode Aligner for the first time, you automatically receive a free 30-day trial when you use Aligner the first time. The trial period allows you to test all functions in CodonCode Aligner. After 30 days, the program converts to the demo version. You can convert the demo and trial versions to a full version at any time by purchasing and entering a license key, or (if your lab or department has purchased licenses) by using the Aligner License Server.

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.

With the demo version of CodonCode Aligner, you can also open existing Aligner projects, like the example projects included in the distribution, and try many of Aligner's functions, like end clipping and assembly. However, you cannot save, export, or print from projects that contain contigs, or after you tried any of the restricted functions (Aligner will warn you first).

Installers for CodonCode Aligner 2.0.6

If you are currently using a licensed version of CodonCode Aligner 1.6.3 or older, you will need a new licence key for this version. Users with a current update and support agreement should already have received a new license key from CodonCode Corporation.

Download CodonCode Aligner 2.0.6 for Mac OS X (18.3M) - Alternate server
( Explorer users: control-click, then choose "Download Link to Disk" from the popup menu)
Requires Mac OS X 10.3.4 or newer.
The download file is a disk image that contains the installer.
Download CodonCode Aligner 2.0.6 for Windows (28.2M) - Alternate server
After downloading, double-click Aligner_Installer.msi to start the installation, and follow the instructions on the screen.
Requires Microsoft Installer (included in Windows XP, downloads for other Windows versions available at the Microsoft website).

Before installing, please make sure to quit CodonCode Aligner if Aligner is running.

Updating to CodonCode Aligner 2.0.6

To update older versions to version 2.0.6, please follow the instructions below.

Please note that if you are upgrading from CodonCode Aligner 1.6.3 or older, you will require a new license key. Users eligible for free upgrades should have received new license keys by email between July and September 2007.

Updating to CodonCode Aligner 2.0.6 on Windows

Quit CodonCode Aligner if Aligner is running.
Open the Control Panels
Select "Add or Remove Programs" (Windows XP) or "Programs - Uninstall Programs" (Vista)
Select "CodonCode Aligner", and click the "Remove" or "Uninstall" button. Wait until the uninstall is complete. Please do not remove any files or folders that may remain after the uninstall
Download the installer for CodonCode Aligner 2.0.6 using the links above
Install the new version at the same location as the previous version (typically in C:\Program Files\).

Updating to CodonCode Aligner 2.0.6 on Mac OS X (10.3 and newer)

Quit CodonCode Aligner if Aligner is running.
Download the installer for CodonCode Aligner 2.0.6 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 for older versions are available on the archive page.