Hey Laiteshwari,

There are different platforms for LefSe analysis, for example via R, Python, and Galaxy. There are many packages available in R for such research (i.e., https://waldronlab.io/lefser/articles/lefser.html, https://rpubs.com/mohsen/lefse_analysis_cleaned_prevalence_phyloseq).

Based on Lefse's result, you can say which of your taxa significantly differs at XYZ levels (at phylum, class, order, and so on). One thing you should keep in mind is that the Lefse plot does not tell you how big is the difference, for that you should perform other statistical analysis.

I hope this helps.

Milan

Thanks Mr. Milan, satisfied with your reply.