How to calculate Ka/Ks ratios

[timpanister]

Hi,

Can Ka/Ks ratio be calculated for within species ie polymorphism data?

[Cat]

For a few cases maybe, but probably not for most. Ka is the number of non-synonymous base changes and Ks is the number of synonymous base changes in the same gene. In most cases of within species gene polymorphism no synonymous base changes present (say Ka=1 and Ks= 0, then ratio is 1/0, which cannot be).