Hi Justin,

The '?' symbols you see are caused by the fact that in your nucleotide alignment, gaps span codon boundaries --  for example around nucleotide position 1125:




HyPhy will read this as codons AG-, --A, AAA for sequence 1 for instance, and both AG- and --A map to "ambiguous" (i.e. ?) amino acids.

I would check your alignment to make sure the gaps are correctly placed, because they could affect Datamonkey inference.

Best,
Sergei