Hi @Crispy13,
My understanding is that defining a "subclass" is optional. That is when you can subdivide your data in such a way that your...
subclasses should be subsidiaries or subdivisions of a single Class
Check out the phrasing of these posts form the LEfSe-users group and QIIME 2 forum:
- LefSe Class and Subclass
- how does subclass influence the LEfSe result? This is where the above quote is from
- Lefse after QIIME2 Note the mention of needing 2-3 rows at the top of your LEfSe formatted input file, that is you may or may not have a subclass for your data.
-Best wishes!