Hi Gibs,
Thank you for the reply.
I deliberately replaced the underscore with the spaces, since when I’m calculating alpha diversity with a tree, I found the tips of the tree are stored in the python script in the format with only spaces. So in order to align the feature table and the tree, I make sure the feature names are with spaces only. I talked about it in an earlier post from me: All ``feature_ids`` must be present as tip names in ``phylogeny``. Tips missing when converting the newick tree to qza format
With the fake data I posted here, you have no problem calculating the alpha diversity with Faith distance.
But I ran into problems when calculating the unifrac diversity, and I haven’t seen this error message in the forum before
Angel