Question: Kaks Calculator
2
gravatar for figo
7.4 years ago by
figo200
figo200 wrote:

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

• 5.7k views
ADD COMMENTlink modified 7.4 years ago by Botond Sipos1.7k • written 7.4 years ago by figo200
5
gravatar for Botond Sipos
7.4 years ago by
Botond Sipos1.7k
United Kingdom
Botond Sipos1.7k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Botond Sipos1.7k

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

ADD REPLYlink written 7.4 years ago by figo200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1029 users visited in the last hour