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I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, and 300 samples. My phylogenetic tree only considers the most important 500 taxa. My questions are:

  1. Do I ignore the 2500 taxa that were not considered in the phylogenetic tree?
  2. Is their a package in R that deals with this kind of missing data?
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    $\begingroup$ Welcome, your request is a bit unusual. Could you provide details about the way you have built the tree please? I don't know of any tree package that would remove OTUs unless you are collapsing clades. $\endgroup$ – Michael Sep 4 '19 at 8:13
  • $\begingroup$ Sorry I am also a bit confusd by this "which has about 3000 taxa, 300 samples" ... that seems to imply 10 taxa per sample .. is this metagenomics? $\endgroup$ – Michael Sep 4 '19 at 11:19
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To calculate the unifrac distance you need the phylogenetic tree. If you only have it for 500 taxa then you can only calculate it for those taxa.

It is impossible to impute the phylogenetic tree without knowing the sequence on which the taxa is based. But if you know it then you can calculate the phylogenetic tree for the 3k taxa you have.

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