How to calculate the p-value (?) using LRT from codeml output ?

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3.6 years ago

sunnykevin97 ▴ 990

HI

I constructed LRT

ΔLRT = 2×(lnL1 - lnL0) 
         = (2×(-1114.093613 − (-1116.287406)) = 4.387586.

The degree of freedom is 1 (np1 - np0 = 20 - 19)  = 1

How do I calculate the p-value ?

Little confused,

Suggestions please.

alignment DNA Gene RNA • 1.3k views

ADD COMMENT • link 3.6 years ago by sunnykevin97 ▴ 990

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Hey check out this tutorial..

https://evosite3d.blogspot.com/2011/09/identifying-positive-selection-in.html

ADD REPLY • link 3.6 years ago by pinn ▴ 210

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Seems good tutorial, I'm not so clear ... Clear explanation is needed in understanding/calculating the p-value (?) using the LRT and df score.

ADD REPLY • link 3.6 years ago by sunnykevin97 ▴ 990

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Calculating p-value using dchisq() in R.

dchisq(4.387586,1) 
p-value 0.02123465

ADD REPLY • link 3.6 years ago by sunnykevin97 ▴ 990

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