I am having a relative abundance files with two classes, samples no subclasses. When i run Lefse in Galaxy Site, I am getting only the features from one class instead of two. I am attaching the input files and the plot results figure for you reference.
Lefse.tsv (88.5 KB)
The interpretation there is that all of the differentially abundant features have higher abundance in the jss_b1 group compared to the other group. If there was a feature that was significantly more abundant in the other group, it would show up as another color.
I hope that helps!