CodonCode Aligner Forum

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...

CodonCode Aligner 10.0.3 was released on May 24, 2023. This update fixes several bugs. This is a free update for users of CodonCode Aligner version 10.0.2. Users of older versions of CodonCode Aligner with expired update and support agreements need to purchase an update to use this version. Installe...

CodonCode Aligner 10.0.2 was released on February 18, 2022. This update fixes several minor bugs, and includes accuracy improvements for separating alleles. This is a free update for users of CodonCode Aligner version 10.0.1. Users of older versions of CodonCode Aligner with expired update and suppo...

CodonCode Aligner 10.0.1 was released on December 17, 2021. CodonCode Aligner version 10 introduces several new features and improvements: virtual restriction cloning; linear and circular sequence maps to display features and restriction sites; a new function to separate alleles in diploid NGS data;...