Dear sergei,

I made a mistake about the paper population genetics of dn/ds, the author is sergey kryazhimiskiy. On the other hand, data monkey sets calculate the ratio dn/ds, and other programs the ratio ds/dn, could you help me to understand how do they work? Analyzing a sequence data by datamonkey I get a ratio of dn/ds= 0.398 and using the snap pram which is ds/dn I get   4.5. my confusion is because I am followed a methodology of one paper to calculate positive selective pressure, they said that w= ds/dn  and report values of 3 that they interpret as a positive selection (using snap), but processing they sequences in data monkey I get dn/ds= 0.9wihtout evidence of positive selection. Could you help me to clear up it?

Thanks,

Lauro.

Hi Lauro,

dN/dS is by far the more common measure; it is also sometimes called Ka/Ks. Please take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for background. dS/dN should, clearly, be the inverse of dN/dS, i.e. high dN/dS (>1) indicates possible positive selection, while high dS/dN (>1) implies low dN/dS (< 1), and hence, negative selection.

Best,
Sergei