How can I calculate p value for rate analysis of particular lineage?
0
0
Entering edit mode
5.8 years ago
evo_genomics ▴ 60

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

rate analysis evolution selection P value • 1.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 2251 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6