Creating a rooted insertion tree from a combined BIOM table

Hi I have used redbiom to pull out a large set of data from Qiita. I have downloaded this set of data as a biom table. I want to run a weighted beta diversity analysis on this set of data combined with my set of data, but I require a rooted tree to do that. I want to use the SEPP plugin to create a rooted insertion tree. But, I’m unsure of how to create a rooted tree from this biom table because some of the studies don’t have reference hit sequences (which are required for the SEPP plugin). Is there a way I can go from 2 BIOM tables to a combined BIOM table (I used feature table merge to do this, is this correct?) to one reference hit sequences file to a rooted tree? Thank you.

Hi @Stephanieorch,

Unless those tables use closed-reference OTUs you can't actually do anything like phylogenetic analysis as the sequences do not exist :frowning:

Yep, that's how you do it!

This is very unlikely to work, as unless the feature-IDs are shared, or represent something with a known reference sequence, you simply lack the information you need.

It seems strange that a Qiita study would be missing this information, so my money is that there is a set of representative sequences for them somewhere, but I'm not sure where (they might be Greengenes OTUs already for example).

What do you feature IDs look like? (Third tab of the feature-table summarize visualization has that info).

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They were all in Qiita but due to the large sample size I ended up just using my biom table to create a new FASTA file. Thank you!

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