Hi

I have a couple of (perhaps blindingly) obvious questions, but after numerous analyses using Hyphy/Datamoney and looking at the guides and boards, I still haven't found a way to get a print out of:

1) The number of synonymous and nonsynonymous substitutions per codon site, and
2) The overall codon tree length (as opposed to subs/nucleotide).

What are the necessary steps to achieve this? (Dataset of 35 sequences and 210 codon sites).

Also, Hyphy tends to crash after I try and save results to file...is this anything to do with an urgent need to upgrade my (Windows)computer?

Thank you very much in advance,

Jo  

Hi Sergei

That's great, thank you. However is there a way to get a print out of the number of nonsynonymous and synonymous subistitutions for each codon site? I think you can do this using the SLAC method in Datamonkey, e.g:

Codon      Observed S       Observed NS
                Changes            Changes      
1             1                      0
2             3                      1
3             1                      0
etc

Also, will this depend upon the selection method used (SLAC,REL,FEL),  or is there a quick and general way of calculating the above?

Thanks!
Jo