If you can not open your Aligner project any more because there was a problem when saving, you can restore projects by using the backup file (ending in .bak). This can happen for example when Aligner runs out of memory, or your laptop runs out of battery.
To restore your project, please follow these instructions:
1.) Quit CodonCode Aligner
2.) Rename the project file that you can not open any more (e.g. add and "_bad" to the name)
3.) Locate the backup file. It ends in .bak, and should be at the place where you saved your project.
4.) Rename the .bak file by removing the ".bak" extension. The file should now end in .ccap like a regular CodonCode Aligner project.
5.) You should be able to open this file as a regular project in CodonCode Aligner