CodonCode Aligner 4.0.1 was released on May 3, 2012. This version adds many new features, including improved support for large projects, support for FASTQ and SAM files, a zoomable contig overview with coverage panel, new tree functionality, and more. For a description of new features, please visit www.codoncode.com/aligner/new.htm. A discussion of some of the speed improvements for larger projects can be found on the CodonCode Aligner Blog.
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 will receive a new license key by email. 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.