I’m very new to galaxy and have been trying to generate cladogram for a microbiome dataset I have. However, I can’t seem to generate the appropriate graph that depicts the relationship between my samples. I’ve attached the cladogram that I’ve generated using my data set (partial data set also shown). It seems to be focused only on one of the groups.
My question/situation’s kinda silly but any input on how I could improve my data set to get the something like the reference cladogram would be very much appreciated.
Apologies, but I am a little confused by your question. The top result looks perfectly fine to me. Did you want to re-generate the bottom plot exactly?
Thanks for your response! My question is a bit confusing to be honest haha.
One of the things I found odd in my cladogram is that it doesn’t seem to have “Clostridia” as one of the depicted levels in the figure even though my data set consist mainly of that. Comparing the first cladogram to the reference cladogram, the reference cladogram depicts the different taxa present (ex: Firmicutes then Clostridia, followed by Clostridiales, etc.) while the first one doesn’t. Is there a way to force the system so that certain levels (ex: Clostridia) show in my cladogram?
Ah okay, thanks for the clarification. LEfSe does not to my knowledge have that type of functionality on the cladogram function. However, the backend of that function relies on GraPhlAn in which you are able to do everything you want to do with the tree figure. Here is GraPhlAn’s tutorial - I hope this helps!!
