I have made Heatmap using Hclust2.py script of your software but I want to know the meaning of the options S_dist_f and f_dist_s where we have to select from the 3 available options which are euclidian, braycurtis and correlation. I am attaching image of the Heatmap that I created, I request you to give a little explanation how can I create a meaningfull Hmap using these options? I wanted the Blue and red blocks that I took as metadata(surface type) to cluster together which I do not see happening here, I was wondering that is because I have selected the wrong distance options. I hope that I am able to explain my problem to you clearly.
One more thing I want to ask is that there is a flag -ftop n which gives the top n number of features in the heatmap but if I want the top 100 features/clades with their abundances in the form of a profile.txt file then for that, is there any method?