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MEME interpretation - 0 branches? #1721
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Dear @glitterseaworms, This is a bit counterintuitive, but here's an explanation. For the site you provide as an example, When MEME calculates which, if any, branches may be subject to selection, it attempts to estimate a Bayes Factor (empirical Bayes), that β > α (or ω > 1) at that branch. However, the PRIOR probability for ω > 1 is estimated to be exactly 1, which makes the prior odds (needed to calculate Bayes Factors) infinite. So Hope this helps, |
Ah ok thanks for the explanation. In that case, would you say it is reasonable to hypothesize that the site may still be under diversifying selection then? |
Dear @glitterseaworms, Yes, and the selection is pervasive (applies to all branches), or at least we have no ability to resolve it further down to specific branches. Best, |
Thank you kindly for your help. I really appreciate you! |
Hello, I was wondering if we should not consider codon sites that have significant p-values but have 0 branches listed? For example:
Based on the likelihood ratio test, episodic diversifying selection has acted on 1 sites in this dataset (p≤0.05).
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