Hi, I begin to practice Hyphy2.1.2 on window XP follow your Workshop:Vancouver2011:SelectionAnalyses course.
When 1.2 Running REL and after 2 Choose Genetic Code : Universal, the program show the  window:branch lengths:condon model/nucleotide model, which is different from your lesson. And after closed condon model/nucleotide model, the program show Model string:. If inputted Default, hyphy show the window Amino Acid Class Model : Default. But after that, it show the bar:Run out of input in buffer during a redirected standard input read. Current task has been terminated. Would you like to see the remaining error meddages, if there are any?
After Y, it showed:
Model string:default
How many datafiles are to be analyzed (>=1):?
Reading input file 1/1

______________READ THE FOLLOWING DATA______________
19 species:{Rabensburg_isolate,WNFCG,SPU116_89,KUNCG,Italy_1998_equine,PaAn001,KN38
29,RO97_50,VLG_4,Ast99,PaH001,Mex03,IS_98,HNY1999,NY99_eqhs,NY99_flamingo,EthAn4
766,Chin_01,Eg101};
Total Sites:1857;
Distinct Sites:357

A tree was found in the data file:
((((((((((Rabensburg_isolate,(WNFCG,SPU116_89)),KUNCG),(EthAn4766,(Chin_01,Eg101
))),(((Italy_1998_equine,PaAn001),(RO97_50,VLG_4)),KN3829)),Ast99),PaH001),IS_98
),Mex03),NY99_flamingo),HNY1999,NY99_eqhs)

Would you like to use it:(Y/N)?


Please enter a 6 character model designation (e.g:010010 defines HKY85):
Please enter a 6 character model designation (e.g:010010 defines HKY85):
Please enter a 6 character model designation (e.g:010010 defines HKY85):
Please enter a 6 character model designation (e.g:010010 defines HKY85):
Please enter a 6 character model designation (e.g:010010 defines HKY85):
Please enter a 6 character model designation (e.g:010010 defines HKY85):

I changed the File:WN NS3.fas to nexus and separated the sequence and tree, but the progress all failed.  Vancouver2011:SelectionAnalyses course is the simplest course for Hyphy I found on line. So please tell me how to continue practicing?
Thanks a lot!

Hi, Sergi. Thank you very much for your timely replay and update. The program runs well. I think I need learn more about Hyphy and positive selection.
Have a nice weekend,