Hi, Sergei and Simon
I tried to use Hyphy to do the ancestral reconstruction after I run the NonSynonymous/Constant/Dual models. When I click the results-->Ancestral Sequences, I saw a window showing 'nuc_lf' and 'lf'. I guess the first one is for recreating nucleotide seqs and the latter is for amino acid. However, doesn't matter which option I chose, the hyphy program will close suddenly.

I am using Hyphy 1.0 windows version.

Could you help me figure out what is wrong here? Or is it possible to do ancestral reconstruction for codon sequences.

Thanks a lot in advance.

Jingjing