I have identified species that characterize the differences between cases and controls in my study.
There were several taxa that had LDA>2 (lefSe.pdf)
When I generated the accompanying cladogram (cladogramm.pdf),
some of the top species were absent in it.
For example, ‘Eubacterium_sp_CAG_180’ and ‘Prevotella_sp_AM42_24’ were absent in the cladogram.
I also checked to see if they were represented at the genus level or any higher-level branch of the phylogeny that can include them. The cladogram had no such higher-level taxa.
Can you, please, help me with this issue?