Wich program inside galagy should I use to compare two or more samples of microbiome (16S).
Welcome @Federico_Sisti
We have tutorials for 16S analysis here to get your started. →
Once you are oriented, you can try adapting the workflows used in the tutorials, or you can create or extract your own. This is a good tutorial to learn about Galaxy in general plus workflows.
From there you can expand your search to Public Workflows hosted by the community. Try searching here with the keyword 16S to find the choices.
Hope this helps! 