Build tree to calculate beta diversity
Can you give a little more information about what tools you are using? How did you generate the OTU table etc?
FastTree is a very simple tool to generate a decent phylogeny. If you have the sequences of each OTU, you can align them in MegaX with muscle, or simply using muscle from the command line if you prefer. You can then generate the tree with this command (presuming you are on windows):
FastTree.exe -gtr -nt &lt; aligned_sequences.fasta &gt; otus_tree.tre 

I hope that helps!