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dN/dS calculation (Read 2168 times)

ursulla82

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dN/dS calculation
Feb 3^rd, 2010 at 1:52am

Hi,

I would like to know how the mean dN/dS is calculated. I tried to calculate it using the csv file and excel but my mean dN/dS is different from the one given directly by hyphy. I summed all the dN then I summed all the dS, then I calculated the ratio.

I have got a second question, about datamonkey, how can I get the mean dN/dS with IFEL and FEL? IT seems that only SLAC gives this value.

Thanks a lot
Ursulla

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Sergei

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Re: dN/dS calculation
Reply #1 - Feb 3^rd, 2010 at 6:48am

Dear Ursulla,

The 'mean' dN/dS reported by SLAC is estimated by maximum likelihood from the entire alignment. One should NOT attempt to obtain mean dN/dS by averaging site-by-site estimates, primarily because the contribution of each site to the mean dN/dS is not equal (e.g. more variable/informative sites will have a greater effect). If you are after a mean dN/dS estimate, please follow the exercises described in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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