how to calculate the dN/dS for a orthologus gene family ?

[yayahoho1]

Hi, I'm pretty new to hyphy and need some help from you. I have 10 bacterial genomes and got 1000 single-copy orthologus gene families by orthofinder. Now I want to calcaulate the dN/dS for a orthologus gene family by hyphy. However, I was wondering if (1) which method of hyphy I should take ? (2) about tree file, gene tree of a orthologus gene famliy or species tree(by using the concatenation of all single-copy orthologus gene families ) , which one is better?

Thanks Yilin

[spond]

Dear @yayahoho1,

We have written several tutorials that you could look at to decide what is the best approach to take. Generally, calculating an average dN/dS per gene is not useful, unless your data are of exceptionally low divergence. As a default analysis to estimate the distribution of dN/dS across sites and branches, I would recommend our busted method.

Best, Sergei

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