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Branch Site Test Of Paml

Hi All,

I am trying to understand the branch site test or the model A (NSsites=2,fixomega =0 and omega 1 ) and the null model as Nssites=2,fixomega=1 and omega=1). I ran the codeml, but i was wondering that the output of the codeml file doesn't contain any information of omega on branches i.e. the foreground branch and background branch. You get information like this( i just pasted important lines dues to space constraints).

lnL(ntime: 33 np: 38): -1032.376871 +0.000000 kappa (ts/tv) = 4.26266 dN/dS (w) for site classes (K=4) site class 0 1 2a 2b proportion 0.47831 0.38910 0.07312 0.05948 background w 0.00000 1.00000 0.00000 1.00000 foreground w 0.00000 1.00000 999.00000 999.00000

So where is the omega value of the foreground and background branch. I can understand that i have to compare the lnL of model A with the null model and get the p significance value , but where is the information of the branches omega .How to figure out that.

Regards

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updated by David W David W • written by figo figo

1 answer

There are actually four omega (given as w) values for the foreground and the background branches

N/dS (w) for site classes (K=4) 

 site class          0    1      2a         2b 
 proportion    0.47831 0.38910 0.07312     0.05948 
 background w  0.00000 1.00000 0.00000     1.00000 
 foreground w  0.00000 1.00000 999.00000   999.00000

So, if you belive the analysis most sites are being conserved or evolving as per the neutral expectation (classes 0 and 1) but a few sites that are conserved in the background braches are subject to very strong postive selection in the foreground branches (classes 2a and 2b).

Elsewhere in the file there will be a list of results fo the probability with which each site has been assigned to a class.

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written by David W David W

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