Hi Pablo,

This error means that your alignment contains sequences of different alphabets, for example both nucleic and amino, or contains some symbols UGENE doesn't know how to process (we call this 'raw' alphabet) In this case its impossible to make an alignment since you can't assign scores to match operation. UGENE reports error when you try to create such files.

However I think that there is a good chance here for improvement from our side. Could you attach the alignment so we can analyze the error in details?

BTW, I would not suggest using Muscle 4 today as mainstream version of the alignment algorithm. Muscle 3 is significantly faster and more stable. Muscle 4 is just an preview release.

BTW2, Note that starting from version 1.6.1 UGENE contains  KAlign algorithm. We recommend using it for a huge number of sequences (~100k) when Muscle becomes too slow to do the job