Sergei
|
Dear Albert,
[quote author=avilella link=1126272230/0#0 date=1126272230]Interpreting rel. dS units between HYPHY and PAML
I have a dataset for which I have tested the Local/FR and Global/M0 models of codons in HYPHY and PAML for the Codon Frequency models that they share in their implementation, and found that:
Both programs give exactly (to the fourth/fifth decimal) the same results, in the Likelihood Value, R/omegas, dN/dS values, tree branch lengths, etc.
Both programs use, as expected, different units in the branch lengths of the estimated tree, in a relation of 3 to 1 or to number of changes per codon or per nucleotide.
Both programs use different units in the dS (and dN for Local/FR) branch lengths that don't follow a 3 to 1 relationship, and this relation changes between the different shared Codon Frequency models or between subsets of the data.
[/quote]
HyPhy reports [tt]synRate, nonSynRate[/tt] straight from the rate matrix, i.e. these quantities are not quite dS and dN. The first thing you can try is look [url]http://www.hyphy.org/cgi-bin/yabb/YaBB.pl?board=How2;action=display;num=1101838973;start=3#3[/url] for the code which will convert synRate to the expected number of substitutions per codon (or nucleotide) and nonSynRate => to E[nonSyn subs]. These conversions depend on the base composition of the data and thus vary from data set to data set.
This may still not be enough; I am not sure whether or not PAML normalizes the expected substitutions by 'synonymous (or non-synonymous) sites' before reporting dS and dN.
Cheers, Sergei
|