What's new in CodonCode Aligner 9.0

CodonCode Aligner version 9.0 has an improved base view, support for EMBL and Genbank features, new sequence selection functionality, and much more.

Please note that CodonCode Aligner 9 requires a new license key. Version9 is a free upgrade for all users with a current update and support agreement as of October 05, 2019. Other customers can purchase an upgrade to version 9.

Better Base View

CodonCode Aligner 9 introduces a new base view that displays features and restriction enzyme cut sites.

RFLP results

Clicking on a feature will select the features and the bases that it covers. Shift-clicking extends the selection. You can select a restriction fragment by first clicking on the restriction enzyme name, and then shift-clicking on a second enzyme name.

Mouse overs display information about the features and cut sites. A mini map at the top gives an overview of the features and allows quick navigation within the sequence.

The toolbar buttons on the left of the base view contain options to show or hide, or select specific features and enzymes, for example showing only enzymes that cut once.

Sequence Selection Options in Aligner 9


Sequence Selection

Aligner 9.0 adds the functionality to select samples and contigs based on length, name, sequence, direction and assembly status.

This new feature is especially useful when working with large projects and eleminates scrolling to select sequences.

You can use multiple of these selection methods at once by using the option to search in the current selection.

EMBL and Genbank Feature Support

Newly added to Aligner 9.0 is the ability to export sequences in Genbank and EMBL format.

Also, all Genbank and EMBL features are imported in this Aligner version and can be displayed based on user preferences. Features colors are settable and features can be used to navigate and select bases.


  • Select "Range of Bases": Select bases by entering the base numbers to select.
  • Improved clustering speed and accuracy
  • Change feature (tag) colors
  • Edit sample comments in the project view
  • New feature (tag) preferences that allow showing only specifc feature (types) in the project
  • Improved handling of ambiguities when searching for sequences


CodonCode Aligner 9.0 is compatible with Windows 10, macOS Big Sur, and Apple Silicon M1.


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