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How to give alternate rates for dN & dS values? (Read 2503 times)

spa YaBB Newbies Offline Feed your monkey! Posts: 2	How to give alternate rates for dN & dS values? 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
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Sergei

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Re: How to give alternate rates for dN & dS values?
Reply #1 - 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.

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spa YaBB Newbies Offline Feed your monkey! Posts: 2	Re: How to give alternate rates for dN & dS values? Reply #2 - May 17^th, 2011 at 8:48pm Thanks!
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