I am trying to calculate beta diversity using the UniFrac distance on my data, each sample having OTUs values.

To calculate it, I saw it required building a tree with percentages that represented the OTUs. However, I was unable to figure what percentage fit each OTU to build the tree from the instructions I found on the internet.

For example, I saw in this link: http://readiab.org/book/0.1.1/3/1#4.1.2, that they build this tree:

enter image description here

Could you please explain to me how to build the tree?


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 < aligned_sequences.fasta > otus_tree.tre 

I hope that helps!


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