Dear Horacio,

The crashes are definitely a bug - I'll look into that.
Sequence names in HyPhy are more restrictive than usual - in essense they must be valid identifiers (alphanumeric with underscores). '.' is has a special meaning - not unlike the C/C++ syntax. In HyPhy tree_id.branch_id.parameter_id is the way to refer to a model paramater attcahed to a branch in a tree - if '.' is found in the middle of a sequence name, odd behaviour results. I'll put more informative error messages into the code. In the meantime, I'd recommend replacing '.' with underscore in sequence and tree branch names.

Sorry about the inconvenience.

Cheers,
Sergei