Kaks Calculator

Question

[figo]

Hi All

I used the KaKs calculator to calculate the omega value. I got many instances where the omega values are greater then 1. But I have a question, in the next column I see the p-value which has been calculated by the Fisher test whose values are greater then 0.05 for all the KaKs which are greater then 1. How to interpret this, to take the omega values greater then 1 as the values of the positive selection or not. I hope some one who has run this can help me to interpret this results.

Best regards

Answer 1

[Botond Sipos]

The KaKs calculator (probably) performs a Fisher's exact test of selection as described in Zhang et al. (1997). The null hypothesis is neutrality (omega = 1), which in your case is not rejected at the significance level of 0.05. Which in practice means that the test could not detect selection in your dataset.

You could try likelihood-based methods (as implemented in PAML or SLR) which can have more power for detecting selection.

[figo]

Thanks for the answer. Yes, I was also thinking that the Fisher test couldn't find the selection their. Thanks once again.