I found this question as it covers exactly what I would like to do, but somehow bacterial species numbers doesn't match at all when comparing the original diamond alignment file and the extracted document. For example, on the extracted file I can only see 6 bacterial species while in the original diamond file there are at least 40 bacterial species.
What I did was to select the Bacteria node, then select the whole subtree and then use "Extract to new document". This on Megan 6.8.12.
What could I do? what I'd like to do is to grab everything bacteria-related and then perform SEED/COG analysis.