Thank you for your kind explanation and thank you for linking the moving pictures tutorial! It is well explained in the current version of the tutorial.
Now I have the same problem as described here.
For some reason the feature_ids were changed when I created the tree. The metadata.tsv information gets added to the feature_id's names. However I am fairly sure that I can solve this myself, so there is no need for you to look into it. I will post the solution later!
Thank you and have a nice day!