Extracting sub taxa as "new document" results in very different taxonomy tree

Hello there,

I meganized and imported a diamond blast .daa file into Megan 6.10.5. In that file most of my taxa belong to bacteria. I want to exclude everything else. I am aware of the extract nodes as “new document” possibility.

However, when I do that, the extracted taxa branch out very differently.
As an example, Opisthokonta result in 16 further nodes. If I extract that branch into a new document, the tree opens to 786 nodes.
How can that happen?
And is it possible to extract the SEED functions for a specified group?

Greetings and thank you!

The reads that are extracted are then subjected to a separate taxonomic analysis, using the same parameters as used for the original analysis.
This will not necessarily result in exactly the same result, particularly if you use a relative filter such as MinSupportPercent. So you may need to adjust the analysis parameters after extracting the data.
Does that solve the problem?