CodonCode Aligner 7.0.1 released

Announcement of new version releases and related information.

CodonCode Aligner 7.0.1 released

Postby Peter Richterich » Thu Feb 16, 2017 4:43 pm

CodonCode Aligner 7.0.1 was released on February 16, 2017. This version fixes bugs introduced in CodonCode Aligner 6.0.1.

CodonCode Aligner version 7 adds a new function for RFLP (Restriction Fragment Length Polymorphism) analysis. It also adds a new "built-in algorithm" for NGS assembly of bacterial genome-sized projects that can generate significantly longer contigs. For more information about new features in CodonCode Aligner version 7, please visit

Version 7 requires a new license key. Version 7.0 is a free upgrade for all users with a current update and support agreement as of February 16, 2017. Users upgrading from older versions will require a new license key, which may require the purchase of an upgrade if the support agreement has expired. 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 If you are updating from an older version of CodonCode Aligner, please make sure to follow the update instructions on the download page.

Operating System Requirements
- Mac OS X 10.7.4 or newer (including OS X 10.12, "Sierra"); OS X 10.8 or newer recommended
- Windows XP or newer (including Windows 10)

Other changes
Both the Windows and Mac OS X versions of CodonCode Aligner 7.0.1 have a number of "under the hood" changes that have been requested by customers and improve performance. On OS X, CodonCode Aligner now contains a "bundled" JRE, and does not require the separate installation of an outdated Java version anymore. This required that support for OS X 10.6 was dropped.
On Windows, the "bundled" JRE is now the original current Oracle version, instead of the Excelsior Jet JRE that was used up until version 6.0.2. We had switched to using Excelsior Jet several years ago to eliminate problems with increasing the memory available to CodonCode Aligner that many users were experiencing. However, recent tests have indicated that these issues have been fully resolved in the current Java versions, at least on 64-bit versions of Windows. The bundled Oracle JRE has substantially better performance than Excelsior Jet when working with projects that require more than 1 to 1.5 GB or memory, both in respect to memory use and to speed. Users who upgrade to CodonCode Aligner 7 on 64-bit Windows may notice a substantial performance increase when working with large projects.
Users on 32-bit Windows may notice that the maximum memory available to CodonCode Aligner is now limited to 1 GB, compared to 1.4 GB in earlier versions. This change was necessary since the 32-bit Java version sometimes fails to start if more memory is requested than what is available as a "contiguous block". In this case, absolutely nothing happens when users try to open CodonCode Aligner. To avoid this problem, the maximum memory that CodonCode Aligner will request on 32-bit Windows is limited to 1 GB or 90% of available memory, whichever is less. In theory, this limit can be overcome through the use of a settings file. However, it is strongly suggested to rather use 64-bit Windows versions when working with large projects that require more than 1 GB of memory. Please contact CodonCode Corporation with any questions about this issue.
Peter Richterich
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