NRI/NTI analysis in qiime2?

Has anyone done an NRI/NTI analysis (16S) using QIIME2 and is this a possibility?

I saw qiime1 has a relatedness.py script and I know you can convert between the two versions, but I’m not sure how to efficiently group (I’m guessing you could make files yourself that list the taxa you’re interested in but I was hoping there was a faster way).
I didn’t see anything for qiime2 though. Also, if you were going to this, has anyone tried also doing it for fungal ITS data (using ghost tree plugin since the ITS tree is not very accurate I’ve read)?

Any thoughts on this would be appreciated, thanks!

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I don’t think there is a qiime 2 plug-in to do this (yet!), but I have done it with ASVs outside of Qiime and it works great. If you know R, I would recommend the picante package for this job (picante PDF).

Yes! It works great… with the usual caveat that the ITS trees are imperfect.
(I would argue that NTI is one of the best things you can do with a ITS tree, as the accuracy of local phylogeny should be pretty good.)

Here’s the paper where I use NTI and βNTI on both 16S and ITS data.

Colin

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Thanks! The issue with picante is that it can’t seem to handle large trees, and I was able to prune/filter trees in qiime1, but in qiime2 the tip names don’t match up so you can’t make a file of “tips to keep.” Is there a way to filter the qiime2 trees like in qiime1 so you can look into specific groups of bacteria/fungi or maybe cut out the rare taxa?

Actually it seems these two links below will answer what I was confused about (how to get a smaller tree with labels that match the taxa names in the abundance file) in case anyone sees this!


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