Question: How can I calculate p value for rate analysis of particular lineage?
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3.9 years ago by
evo_genomics40
Pakistan
evo_genomics40 wrote:

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(dN)=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

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