Clarification about "Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros"

[jp.fland...@gmail.com]

I read that in version 1.6.7:

"Temporarily disable AU test due to unresolved numerical issue when bp-rell are all zeros"

Does this mean that the AU test is _only_ affected in version 1.6.7 or does this occurs in previous versions ?

JP Flandrois LBBE-UMR5558 Lyon, France

[Minh Bui]

Hi JP again,

Unfortunately this affects earlier versions, when a tree has significantly worse log-likelihoods than the ML tree but the AU test does not return ~0 p-value, because it cannot do the inverse of 0. When the trees do not show much lower likelihoods, then AU p-values can be computed more reliably. So the implementation in IQ-TREE is not entirely buggy, it’s just unclear how the CONSEL author resolved this edge case and that’s why I decided to disable the AU test.

Cheers

Minh

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