The Highlight Difference Submenu as described on page 21 of the MEGAN v6.5.9 manual is missing from both the Mac OSX and Linux versions:
Have you used this feature in MEGAN5?
This feature was removed because it is quite messy to implement.
However, if you really have a need for it, then I will look into adding it to MEGAN6
I haven’t used it in MEGAN5, but I currently have two samples (one is a subset of the other) and I am looking for determining under and over-representation of taxa, based on the proteins in each. The word cloud and normal plots show some differences, but I was looking for a more statistical test than doing it by eye (something along the lines of the Fisher’s Exact test used in BLAST2GO for similar analyses).
I also figured as it features in the manual but not the software, one of them needs to change :).
Adding a set of statistical analyses is high on my list of things to do.
In particular, I will look into implementing the calculation that you mentioned.
I have removed the hight differences description from the manual…