Version 4.0 of CodonCode Aligner introduced a new format for saving projects. Aligner now saves your projects in one file thus being faster and more memory efficient when reading and writing many sequences.
Projects saved in the new format can not be opened with old versions of CodonCode Aligner (3.7.1 and older).
You can still export your project in the old project format from the new Aligner versions. To do so, choose "Export-> Aligner Project (Old Format)" from the "File" menu in CodonCode Aligner. This will allow you to create projects that can be read by old versions.
Projects saved in the old format can still be read by the new versions.