Dear Sergel,

Thank you for your immediate response regarding run times.  I have another question.  I keep getting error messages and don't understand why.  I am using a Nexus file which includes aligned nucleotide sequences with a tree and am running HyPhy in OS 10.3.5.  I can run the data in "stripstopcodons" without a problem.  I have problems when I run the file in "dNdSRateAnalysis."  The program runs, but then when it is done and I try to open the out file, I get an error message that says:

Operation: : is not defined.
Current BL Comand:Build Formula:RUNNING
MG94xREV MODEL COMPARISONS on Macintosh HD:
Users:bpsweeney:Desktop:hyphy data:
Trial3US.dat###########3x3
CLASSES###########+--------------------------------------
+------------------------------+----------------------------------+
Current operation/job has been terminated.

Can you tell me what this could mean?

Thank you,

Beatriz