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?

Much appreciated!

Rosie