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selection at population level (Read 678 times)
Tong@21
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selection at population level
Sep 7th, 2012 at 1:01pm
 
Hi
I am trying to find a signature of selection of my interested gene in 51 populations of one species. I am pretty new in the area so sorry if my questions dose not make any sense  Embarrassed.

I used FUBAR to analyze my sequences I found 1 positive selection and 9 negative selection sites.

My first question is how this method designed which codon is under positive selection or which codon is under negative selection for simple explanation?

Second, how I can I explain the graph in FUBAR analysis? what is the peak mean? I do understand the alpha and beta but not for the posterior mean. I can't find any place to read about the FUBAR, it would be great if you could suggest.

Thank you very much,
Tong
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Sergei
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Datamonkeys are forever...

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Re: selection at population level
Reply #1 - Sep 14th, 2012 at 11:33am
 
Hi Tong,

FUBAR has not yet been published, so we don't have documentation (other than Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login) for it.

Please do the following:

1). Read Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login to gain an understanding of how codon-based model for selection detection work.

2). Use MEME (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login) to screen individual sites for selection. This is our current recommended method.

Sergei
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