How can I calculate p value for rate analysis of particular lineage? I have used Mega 6 for estimation of dN/dS ratio ?
Kindly guide me.
I have used 5 primates (human. Chimp, gorilla etc) orthologous sequence for rate analysis (dN/dS ) using Li Wu Lu method. Now I want to calculate P value for estimated dN/dS of each terminal branch (like for human branch).
I used the following method is it correct?
I wanted to calculate p value for dN/dS ratio of human lineage. I used z test formula mentioned in mega manual i.e. Z = (dN - dS) / SQRT(Var(dS) + Var(dN)).
In (dN - dS), I placed human dN and dS value. For calculation of variance, I used dN and dS value of all the terminal and ancestral lineage branches, e,g Var(human dN, chimpanzee dN, gorilla dN, orangutan dN, human-chimp ancestor dN, human-chimp-gorilla ancestor dN ).
After getting z value I calculated p value using online software.
Thanks
It sounds good. I doubt why only to use the dN and dS values of the terminal OTUs, We need to take into account of the internal branches (hypothetical ancestors). Would you please try datamonkey online tool (http://www.datamonkey.org/) to solve/crosscheck your problem/results?
I take into account, dN and dS value of both terminal and internal branches.
In question I have used ancestral branch word in place of internal branch
Please try the same analysis in Datamonkey server. It gives the P-values for SLAC etc.
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