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normalized dn ds (Read 2911 times)
Eric Ho
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normalized dn ds
Jun 20th, 2012 at 8:06am
 
Hi,

Does anyone know the formula for normalized dn ds?

Appreciated.

Eric.
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Sergei
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Datamonkeys are forever...

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Re: normalized dn ds
Reply #1 - Jun 22nd, 2012 at 11:35am
 
Hi Eric,

Which method is this? For Datamonkey, this value is simply raw dN-dS divided by the total length of the tree (measured in the number of expected substitutions per nucleotide per site).

Sergei
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ksenia
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Re: normalized dn ds
Reply #2 - Feb 5th, 2013 at 1:21am
 
Hi Sergei!
Is this normalization can be applied to dn/ds from  QuickSelectionDetection.bf output?
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Sergei
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Re: normalized dn ds
Reply #3 - Feb 5th, 2013 at 9:07pm
 
Hi Ksenia,

It IS applied to the output of SLAC, e.g. see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login see page 64 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login
Generally you should only be asking if dN != dS with these methods, because site-wise estimates could be quite unreliable.

Sergei
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Division of Biomedical Informatics
School of Medicine
University of California San Diego
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