Hi @zejunyan, the relationship between features and samples are what are represented in the feature table, not the aligned sequences (which are used to create a phylogenetic tree). We don’t have any functionality in QIIME 2 (that I can think of) that would allow you to relabel your features with arbitrary labels (in your case, you want to map them to samples, I think). Can you please confirm this, and let me know if we are on the same page? If so, I will create an issue to put this kind of relabeling on our radar. Thanks! 