How to filter dn/ds of free-ratio model

[노유림]

Dear, All

I am currently conducting a free-ratio model analysis using NCBI's primate ortholog group gene sequences. I collected the dn/ds values of each species and filtered the dataset to only include gene sets with dn/ds < 10. This filtering process excluded too many data sets, leaving me with only 1400 gene sets out of a total of 17000 gene sets.

I am reaching out to you because I have some concerns about the validity of my analysis. I am unsure if I am performing the analysis correctly or if there is an error in my approach. Therefore, I would like to ask for your expert opinion and guidance.

In particular, I would appreciate it if you could advise me on the following:

Is filtering the dataset based on dn/ds > 10 a reasonable approach?
If so, what is the typical range of dn/ds values observed in primate ortholog group gene sequences?
Are there any other factors I should consider when selecting gene sets for analysis?

I would be grateful if you could spare some time to answer my questions. Thank you for your assistance and expertise.

Yoo-Rim