Phylogenetic tree tools

[Antani (Edoardo Scali)]

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.

[Nicholas_Bokulich]

Hello @Antani ,

@Antani

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?

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:

@Antani

I'm working on a metabarcoding dataset of ITS1.

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!

[Antani (Edoardo Scali)]

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!

[colinbrislawn (Colin J Brislawn)]

@Antani

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

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.

[Antani (Edoardo Scali)]

@colinbrislawn Thank you so much for your help and for all the resources you shared with me.

What I would like to do is to obtain a phylogenetic tree after the taxonomic classification, in order to display the annotation of my classified features.

Do you have any suggestions for this?

Thank you so much for your help.

[colinbrislawn (Colin J Brislawn)]

@Antani

What I would like to do is to obtain a phylogenetic tree after the taxonomic classification, in order to display the annotation of my classified features.

Do you have any suggestions for this?

Kind of. But not really.

When you have ITS reads, it's had to build a reliable tree for the reasons outlined here:

Analysing fungal ITS data - questions about the pipeline - phylogenetic analysis

Hi @Cat , This is sort of true — ITS alignments are sometimes used for examining phylogeny of closely related fungal species. Thus, fungal taxonomy papers (which are generally concerned with parsing closely related species/groups) will sometimes use this for comparison of isolated strains. Indeed it is. In a mycobiome study you are almost inevitably comparing fungi from highly divergent groups. ITS will not generate a reliable alignment/phylogeny for such divergent groups. As a non-coding r…

So you can push your ITS reads through a MSA -> treebuilding pipeline, but the results will be trash highly stochastic and unreliable.

What sort of figure do you want to make with the tree? Perhaps there is another way to get there, and we can plan for that.

[Antani (Edoardo Scali)]

@colinbrislawn
Basically, I would like to make the tree in order to assess where are placed the sequences classified only at kingdome level as "Fungi". I want to see if the are sparse amongs all the other clades or they fall in the same branch.

[colinbrislawn (Colin J Brislawn)]

So you are interested in relatively unclassified species?

If this is your question, I suppose this might work OK with an MSA:

• are all my k_fungi;p_? closely related to each other in one big group, or from many groups?

But, you could also do a blast or vsearch search and see if all your results are returning the same top hit, or do a vsearch all-vs-all alignment and see how similar these k_fungi;p_? reads are to each other. (No MSA needed!)

If this is your question, it will not work well:

• How related are the different groups of k_fungi;p_? I found?

[Antani (Edoardo Scali)]

@colinbrislawn thank you so much for your help.
I've tryed to use quume 2 phylogeny plugin, but what I've obtained is a huge circular tree with any annotation. Do you have any suggestion about how to use the biom classification (e.g. k_fungi;p_?) for annotating the tree?

Thank you for your help.

[colinbrislawn (Colin J Brislawn)]

How did you build the tree? For whatever program you used, we are looking for an input that would let you pass in taxonomy generated with another program and some settings that would display that taxonomy on the plotted tree.

EDIT: While we are talking about viewing phylogenetic trees, this is probably a good place to highlight empress. There is even a little empress demo, by Mike Robeson, in one of the QIIME 2 workshop videos.

[Antani (Edoardo Scali)]

Here is the code I've used for buildfing the phylogenetic tree:

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences repseqs.qza
--o-alignment aligned-rep-seqs.qza
--o-masked-alignment masked-aligned-rep-seqs.qza
--o-tree unrooted-tree.qza
--o-rooted-tree rooted-tree.qza

Thank you so much for your suggestion about empress. I will try working with it and I'll be back to you if I encounter further difficultyes.