Information-Weighted Sequence Alignment (IWSA) for historical linguistics.
I am currently in the process of adding basic usage information to the Wiki. The basic behaviour and usage of all classes with main methods is described there already.
The code is largely self-documenting through human-readable names, and errors will usually be easy to trace to an unmet assumption (undefined language codes, wrong file names, etc.). Still, it might be best to start with the usage examples given in the Wiki.