Dear Jennifer,

There are three things you can try

(1). Run the model selection analysis on your machine using a HyPhy standard analysis. Choose Standard Analyses:Model Comparison:NucModelCompare.bf and use the following options for successive prompt
- Global
- Once
- Choose Data file and tree
- 0.0002
- choose a file to save results to (make a new directory to contain this file, because HyPhy will write out 203 files with a model fit for every model it tries).

  The best model will be printed at the end of the run (use the first printed model - it'll be the same one that Datamonkey would report).

(2). Use the ciliate genetic code (only one stop codon there: TGA) if you only have TAA or TAG stop codons
(3). Use a HyPhy standard analysis (Standard Analyses:DataFileTools:StripStopCodons.bf) to strip out stop codons before submitting to DataMonkey

HTH,
Sergei