Phylogenetic tree tools

Hello everybody,
I'm working on a metabarcoding dataset of ITS1. I just finished classifying my sequences and plotted how my community fared with taxa barplots.
At this point I would also like to create a phylogenetic tree that also contains the highest possible taxonomic classification. Do you have any qiime 2 tools to suggest that can help me in this job?

Thank you very much for your suggestions.

Hello @Antani ,

Yes, QIIME 2 has several tools for this — an entire plugin, in fact (q2-phylogeny). You can check out the online documentation for more details on this plugin and its methods.

However, what I want to highlight is this:

ITS is non-coding, hence with a high mutation rate and not a phylogenetically informative region (except for rather closely related groups, e.g., at species and strain level). Hence, I would recommend avoiding phylogeny building altogether for ITS as you will get an uninformative tree.

Good luck!

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Dear @Nicholas_Bokulich,
Thank you so much for all the suggestions.

Blockquote
Yes, QIIME 2 has several tools for this — an entire plugin, in fact (q2-phylogeny). You can check out the online documentation for more details on this plugin and its methods.

I would like to ask if you also have any graphical tools to recommend for phylogenetic tree representation.

Blockquote
ITS is non-coding, hence with a high mutation rate and not a phylogenetically informative region (except for rather closely related groups, e.g., at species and strain level). Hence, I would recommend avoiding phylogeny building altogether for ITS as you will get an uninformative tree.

Thank you very much for reminding me of this very important thing. Do you have any publications to recommend that ITS is not reliable for phylogeny?

Thank you so much!

I'm not Nick, but I've seen some nice-looking trees plotted with iTol.

I do most downstream analysis in R, so I have made trees using Phyloseq and ggtree.