I have been using DIVERGE (DetectIng Variability in Evolutionary Rates among GEnes) to test for divergence in function across different clades of a protein superfamily.
I have noticed that when using the 2001 algorithm and the 1999 algorithm (although to a lesser extent) I get negative values for thetaML = the Maximum likelihood estimate of the coefficient of functional divergence (normally lies between 0 and 1). I then get an LRT theta value (likelihood ratio test against the null) of ‘-1.#IND00’ or ‘not a number’.
I emailed the developer but had no response yet. I suspect it may have something to do with short branch lengths or something like that…
Has anyone ever used DIVERGE and have some insight as to why this might happen?