3rd codon position missing

[smirarab]

From Karen:

We trie to run it on a dataset (nucleotide level) where we only have the 1rst and 2nd codon pos. included (not the third). Is there an option to tell DiscoVista this? because when trying around we realized that DICSOVISTA assumes always that all 3 codon positions are included? If not can this be implemented? (we also run e.g. datasets on nt level with only the second position...)