Phylogeny result intrepretation

Hello

I performed phylogenetic analysis for my ITS Sequences. I was struggling to intrepret the rooted and unrooted tree result.

How should I replace the OTU id with organism name (Taxanomic assignment) ?. Its really diffcult to intrepret.

Hi @Asha1,

What are your plans for the tree? Some techniques require a rooted tree, some require an unrooted tree. If you’re into the bioinformatics and phylogeny, it probably matters. That said, I saw the coolest visualization about this on twitter yesterday for rooted and unrooted trees, which links to some good additional discussion.

If you just want to run UniFrac or Gneiss or export your tree to something like phylofactor in R, it functionally doesn’t matter a lot as long as you get the semantic type correct.

I wouldn’t do that in QIIME, and would work on that in your visualization software (whatever you’re using for visualization). My experience is that a phylogenetic tree figure is rarely as cool as you expect it to be, unless you have something really specific in mind already.

Best,
Justine

Hello Ma'am

I want to do phylogenetic analysis for ITS as well as 16s rRNA(V3-V4) sequence. I have done reference based fragment insertion phylogenetic analysis for my v3-v4 sequence and ITS Sequence phylogenetic analysis using this method qiime phylogeny align-to-tree-mafft-fasttree

This is the commandline:
qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences rep-seqs.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

Finally, I used itol visualizer to see the phylogeny result for ITS as well as v3-v4 sequence.

Fragment insertion phylogenetic analysis got over for v3-v4 samples. I rectified error after runing commandline with debug.
(qiime2-2019.1) [email protected]:~/miniconda2/envs/qiime2-2019.1/v3-v4_region_result/sp/mo/moraxellaca.taxaplot$ qiime fragment-insertion sepp --i-representative-sequences rep-seqs-dada2.qza --p-threads 40 --p
-alignment-subset-size 1000 --p-placement-subset-size 5000 --o-tree Phylogeny[Rooted] --p-debug --o-placements Placements
Saved Phylogeny[Rooted] to: Phylogeny[Rooted].qza
Saved Placements to: Placements.qza

Rooted tree would be fine for my analysis. I dont have any specific hypothesis to look in to phlogenetic tree right now. My only concern right now is I have to see organism name instead of OTU id.
For example

I am newbie to programming. So, I don't have idea on R programming language.

Could I use itol visualizer for replacing otu id with organism name? or Is there any other visualizer to replace OTU id with organism name?

Thanking you in advance for your suggestions and help.

Hi!
Even if you replace your OTUs with names, you will receive an error since several OTUs will be assigned to the same taxa. So you will need to keep an original hash and attach the name to it.
To get a tree with names instead of OTU hashes before constructing the tree you should run taxonomy assignment and after modify this files:
table.qza (convert to tsv table and then import back after modifications)
taxonomy.qza
rep-seqs.qza
In all files you will need to attach to hashes assigned taxa names.
Manually it will take an entire life to modify it but with R or Python it is not so hard but will take some time to write an appropriate script.

There is no way to do it inside Qiime with current plugins

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Thank so much for your reply ma’am.

Since you told me it takes an entire life. I dont like to give try. If you could share that script for phylogenetic construction in R or python programming language. I would be gratefull to you.

Hi @Asha1,

I just would like to point out that it is very difficult to generate a reliable global sequence alignment across all fungi using fungal ITS (I assume you are referring to fungi). Thus, ITS data are often not appropriate to generate global phylogenies. However, if you are only analyzing closely related taxa, e.g. within genera, you are likely okay. I’ve listed a few good references below. I am sure others will have additional insight too.

  1. Check out the Fungal ITS analysis tutorial.

  2. If you’d like perform phylogeny-based analyses on your ITS data, then I’d highly recommend using Ghost-Tree. More details can be found here.

  3. As an aside, you may also want to consider ITSxpress, to pre-process your data.

I would also highly recommend this article:

-Best wishes
-Mike

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Thank you so much for your reply sir. I will check and get back to you soon.

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