CodonCode Aligner Forum

CodonCode Aligner 12.0.4 was released on October 28, 2025. This version fixes a bug where trace views would not always show the correct selection, and adds a workaround for a problem that some macOS users had, where file dialogs would not be shown when exporting. CodonCode Aligner version 12 introdu...

Several users have reported problem when trying to export sequences from CodonCode Aligner on macOS: they do not see the "Save as" dialog where they can set the file name and directory for the saving. While most CodonCode Aligner users never see this problem, the same problem has been repo...

Aligner License Server 1.2.8 was released on July 22, 2025. Downloads are available at http://www.codoncode.com/aligner/licenseserverhelp.htm . This update fixes a problem related to preference file saving that some Windows users encountered, and is recommended to all Windows users. Users on macOS w...

CodonCode Aligner 12.0.3 was released on June 5, 2025. This version fixes several bugs. CodonCode Aligner version 12 introduced multiple new features and improvements, which includes support for additional cloning methods: TA cloning, blunt end PCR cloning, and direction topoisomerase cloning; a new...

CodonCode Aligner 12.0.1 was released on December 3, 2024. CodonCode Aligner version 12 introduces multiple new features and improvements. These include support for additional cloning methods: TA cloning, blunt end PCR cloning, and direction topoisomerase cloning; a new function to transfer tags bet...

Aligner License Server 1.2.7 was released on October 16, 2024. Downloads are available at http://www.codoncode.com/aligner/licenseserverhelp.htm . This update fixes several bugs. It also includes a workaround for issues encountered on macOS 15 (Sequoia). Please follow the instructions below closely ...

CodonCode Aligner 11.0.3 was released on October 7, 2024. This update solves problems some users encountered on for macOS 15 ('Sequoia"), and fixes several bugs. This is a free update for users of CodonCode Aligner version 11. Users of older versions of CodonCode Aligner with expired update and...

In June 2024, users have reported that BLAST searches from CodonCode Aligner fail. This problem is caused by a change in the internet address parameters that the NCBI BLAST server expects. The problem can be fixed by adding a corrected entry for the BLAST server address (URL) in the CodonCode Aligne...

CodonCode Aligner 11.0.2 was released on November 13, 2023. This update adds support for reading sequence files in .dna format; support for "headless" operation; and fixes several bugs. This is a free update for users of CodonCode Aligner version 11.0.1. Users of older versions of CodonCod...

CodonCode Aligner 11.0.1 was released on July 18, 2023. CodonCode Aligner version 11 introduces several new features and improvements: virtual cloning using Gibson Assembly; synchronization of starts for circular samples; automatic annotation for common features in plasmids; import of GFF files; and...