CodonCode Aligner 4.0.3 was released on June 7, 2012. This version includes several bug fixes and minor improvements, including the ability to export "unformatted" FASTA files (all bases for a sequence are on a single line).
Version 4.0 requires a new license key. Version 4 is a free upgrade for all users with a current update and support agreement as of December 31, 2011; users qualifying for a free upgrade should have received a new license key by email. License keys entered for version 4.0.1 or 4.0.2 will continue to work with version 4.0.3. If you have questions about your license key or support agreement, or would like to provide feedback, please contact CodonCode's support team.
Installers can be downloaded from http://www.codoncode.com/aligner/download.htm. If you are updating from an older version of CodonCode Aligner, please make sure to follow the update instructions on the download page.