Hi
I hope you can help me or explain to me that I am observing.

I have calculated the number of synonymous and non-synonymous substitutions by nei-gojobori method in MEGA. I can see that the dN is 9.9 and the dS is 8.1...I would therefore expect the ratio to be 1.22 (1000 bootstraps...dataset of 204 sequences). However, when I calculate the dN/dS by HyPhy on the same dataset using the SLAC method in the Quickselectiondetection.bf I get a ratio of 0.529. I do believe that the 0.529 is correct because other methods have given the same result. Why is this difference???
I wanted to use the MEGA dN and dS values to make a graph to illustrate the number of dN and dS substitutions per site.

Is there maybe somewhere in HyPhy quickselection.bf that I can fint the dN and dS values with standard error values or is it OK to use the values that I have got from MEGA???

I am in urgent need for help..and dont understand much about this myself....I'm trying :-)

Karoline

Dear Karoline,

You may find section 1.4.3 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login useful. It also provides a standard analysis which computes dN and dS from an alignment.

Cheers,
Sergei

Thank you. I will have a look at it.
But could you please tell me why I see the difference?

and..I can not find the dSdN.bf in my HyPhy program

Dear Karoline,

There are many possibilities as to why you see a difference. For example, traditional NG (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) does not at all account for transition/transverion biases. Generally speaking there is no reason to use NG for dN and dS estimation - there are too many assumptions which we know to be false built into the method.

dNdS.bf is an option under Standard Analyses -> Miscellaneous -> Phylohandbook.bf

Cheers,
Sergei