Changing rooted tree tip lavels from IDs to taxonomy

[SoilRotifer (Mike Robeson)]

Hi @PabloCL,

@PabloCL

Which is a mess. It seems lefser is comparing feature IDs between the categorical levels of the variable I am interested in (Sample type in this case

This seems like a formatting issue... If you'd like to obtain a traditional taxonomy style output from LEfSe (as intended, where different ranks are shown), you might follow the easy approach outlined here. Then feed the output into LEfSe...

If you are trying to obtain LEfSe cladogram output, there is no phylogeny required. That cladogram is simply a hierarchical taxonomic cladogram, not a phylogenetic cladogram.