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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> normalized dn ds http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1340204785 Message started by Eric Ho on Jun 20^th, 2012 at 8:06am

Title: normalized dn ds
Post by Eric Ho on Jun 20^th, 2012 at 8:06am

Hi,

Does anyone know the formula for normalized dn ds?

Appreciated.

Eric.

Title: Re: normalized dn ds
Post by Sergei on Jun 22^nd, 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

Title: Re: normalized dn ds
Post by ksenia on Feb 5^th, 2013 at 1:21am

Hi Sergei!
Is this normalization can be applied to dn/ds from QuickSelectionDetection.bf output?

Title: Re: normalized dn ds
Post by Sergei on Feb 5^th, 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

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Generally you should only be asking if dN != dS with these methods, because site-wise estimates could be quite unreliable.

Sergei