How to open Sequencher projects in CodonCode Aligner

[submitted by email]

CodonCode Aligner cannot read Sequencher project files directly, but it is easy to export Sequencher projects in a file format that CodonCode Aligner can read - the "CAF" file format (for "Common Assembly Format").

To import a Sequencher project into CodonCode Aligner, you must first export the project from Sequencher in CAF format, as follows:

1. Open the project in Sequencher.
2. Select the reads and contigs you want to export (use "Select All" from the "Select" menu to export the entire project).
3. Go to the "File" menu, and select "Export => Selection As Subproject". This will open a "Save" dialog.
4. Click on the "File Format:" pulldown menu, and select "CAF".
5. Use the "New folder" button or icon to create a new folder to export your project to.
6. Choose a name for the exported file. Make sure that the name ends with ".caf".