The non-synonymous/synonymous rate ratio for test in datamonky represents the dn-ds of the entire gene ?

[douluojiaofu]

Dear doctor, Thank you for watching this question!

I'm using datamonky-slac to detect positive selection site,and I get a result.

I have seen in some articles that some researchers believe that the red content below is the dN-dS of the whole gene. I am not sure whether this index is the dN-dS of the whole gene?? If it can not represent the dn-ds of the entire gene ,how can i get the dN-dS of the whole gene by hyphy ?

I would really appreciate it if i could get your help!

[spond]

Dear @douluojiaofu,

The number you circled is the dN/dS ratio estimated from the entire gene (which is what you usually see reported). I don't recommend reporting gene-level dN-dS. The reason SLAC uses site-level dN-dS is because using the difference instead of the ratio allows you to handle dS = 0 cases.

Best, Sergei

[douluojiaofu]

Dear doctor, Thank you for your help! I will report the dN/dS of the positive sites in my article. Thank you again for your help!

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