hy hyphy guys

so, I've run a GY_3x4_HKY85 model fit on a pairwise alignment (402bp; 134 codons)

the omega estimates are identical
the tstv ratios are identical
t in hyphy is 1/3 of paml's, since i'm guessing hyphy calculates it per nucleotide site and paml per codon

question is:

pmal dN dS is 0.033, 1.337
hyphy dN dS is 1.24, 49.79

i.e. a scaling factor of +-37

after a couple of weeks of wrestling the numbers to no avail, i am now in a state of blissful ignorance   about this, but perhaps you guys can shed some light

also, is the "physical sites" approach to S and NS site defintions as per Bierne& Eyre-Walker 2003 implemented in HYPHY at all?

many many thanx as always
gordon

Thanx for the reply Sergei:

I used the nonSynRate and synRate parameters returned after optimising the model?

Here is the output for the gene:

Code:

global globalVariable_TVTS=0.2279625830281183;
treee.orthos.nonSynRate=1.240564691415671;
treee.orthos.synRate=49.92302114247499;
Tree treee=(orthos:0.430686);
 

sweet! thanx sergei i have come right using the code in the post_sns.bf file but also using the corrections as mentioned in Danny's thread here:
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keep well and thanx again for the help