I used HyPHy for a project last year, and am now relearning things.   I've got 12 aligned coding sequences (some pretty diverged), about 1kb each, and want to take a good look at synonymous and non-synonymous changes on each branch. 

Am a bit at sea over the number of possible ways to proceed, but I figured I start by investigating codon subsitution models.

When I fire up codonmodelcompare.bf and select the data file and a tree file,  the run just seems to stop (it writes 'Model rejection level (e.g. 0.05):'  to the console,  and the status bar says 'Waiting for user input').  When I stop the excution and look at the log file I get a fairly long list of things that it could not do.

It seems like I'm missing something fairly basic here.

Thanks for tips.

Jody