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

Dear Jody,

I would suggest you start by plugging your sequences into Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login, for site-by-site dN/dS analyses and Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for branch-by-branch.

We are finishing a book chapter on using HyPhy/Datamonkey for codon selection analyses (within one week it should be done) - if you can wait that long, I'll post a draft and it may answer many of your questions.

Cheers,
Sergei

P.S. CodonModelCompare.bf will simply search for nucleotide substitution biases (e.g. HKY85 vs TrN93 vs REV etc), but coupled to codon models. This is probably NOT what you want.