S2S allows you to save your data in binary or textual files. When you select the "Save Alignment As..." choice in the File menu:
- choose a name ending with ".s2s" for a binary save,
- any other choice will produce a textual save.
Each file format has its own advantages and drawbacks:
- the textual format takes more time to be saved and reloaded. But it is compatible with all the S2S versions. It is also human-readable and searchable by tools like grep or awk
- the binary format is faster to be saved and reloaded. But it is only compatible with the version of S2S which produces it.