CodonCode Aligner Forum

CodonCode Aligner 4.2.1 was released on June 17, 2013. This version introduces support for 64-bit Windows. On 64-bit versions of Windows, CodonCode Aligner 4.2.1 can now use memory beyond the 1.4 GB limit on 32-bit Windows, up to the available amount of physical memory (RAM). Version 4.2.1 also introduces a number of improvements, in particular for large projects, and bug fixes. All users of CodonCode Aligner version 4.0.1-4.1.1 should update to this version.

Version 4.2 is a free upgrade for users of CodonCode Aligner 4.0 and 4.1. License keys entered for version 4.0.1 - 4.1.1 will continue to work with version 4.2.1. Users upgrading from version 3.7.1 or older will need new license keys to use this version. 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.

After upgrading to CodonCode Aligner 4.2.1 on 64-bit Windows, users may need to edit the "Base calling" and "Phrap assembly" preferences. For example, the default location of the base calling program Phred on 64-bit Windows has changed from

• "C:\Program Files (x86)\CodonCode Aligner\Phred-Phrap\workstation_phred.exe" to
• "C:\Program Files\CodonCode Aligner\Phred-Phrap\workstation_phred.exe"

This concerns only users who use CodonCode Aligner's "Call bases", "Assemble with Phrap", or "Analyze Indels" functions.