Cladogram clarification

The result I get when using Lefse analysis amazes me :

  • When producing the cladogram from my data which are expressed in percent
    with total abundances =100 for all samples, the “Bacteria” node (ie its
    sole root) appeared colored, ie as significantly affected by one of the
    treatment as compared to the other one: how could this happen? how
    should it be interpreted?

I would be more grateful if you could help me understand that.

Lefse T6 F344 D60Male FORvsFSham.txt (121.3 KB)

Hi -
Sorry for the late reply! Did you perform the analysis using command line or through Galaxy? When I tested this on Galaxy using default options I got the same cladogram, with Bacteria node uncolored.