Question: do input sequences need to be aligned?

[josephwb]

I notice that all of the example input data with more than 1 sequence are aligned. Is that 1) required or 2) preferred?

[mkandziora]

This is currently required. The program will check the input and if sequences are of uneaqual length will abort. Good point though, to add an automatic alignment step is easy - will add it.

[josephwb]

Thanks for the quick reply.