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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> How to give alternate rates for dN & dS values? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1305566557 Message started by spa on May 16^th, 2011 at 10:22am

Title: How to give alternate rates for dN & dS values?
Post by spa on May 16^th, 2011 at 10:22am

Hi,

I'm performing a positive selection study in which the dN value comes out to be 3.54359 and Normalized dN-dS comes out to be 13.4139. I would like to convert it to the general rate of mutation ( for eg 3.5x10^-4 substitution/site/year). I have 47 sequences. Kindly suggest how to do this.

Thanks

Title: Re: How to give alternate rates for dN & dS values?
Post by Sergei on May 16^th, 2011 at 11:04am

Hi Spa,

Unless you have external information (e.g. dated tips of fossil records), most models that measure dN and dS will confound rates and times, because they are time reversible; hence all you can estimate are substitutions/site along the entire tree (this is the dN value in your case). Normalized dN-dS value simply rescales everything on a per "tree of 1 total substitutions per site" basis.

Sergei

Title: Re: How to give alternate rates for dN & dS values?
Post by spa on May 17^th, 2011 at 8:48pm

Thanks!