Making trees with itol


I am looking to create trees from the exported tree files, and have been successful in this, and in incorporating taxonomy.qza into the tree. However, I have some repeated species in the tree. I know I can collapse features by their taxonomy, and then I will get a collapsed-table.qza. However, this isnt a file used to generate a tree, so Im not sure how best to deal with this.

Thank you so much for the help!


Hello Scott,

If you are familiar with R, the phyloseq function tax_glom() works like that but it returns a collapsed feature table in addition to a collapsed tree. I’m not sure if there is an equivalent in Qiime2, but there should be!

P.S. I’m not sure if this is a qiime2 question, which is perfect to ask here, or an iTOL question, which you can ask over here. 🤷


thanks so much for the reply! ill look into that option and ask on ITOL.



OK great!

I’m posting again because I think this is totally a valid Qiime2 question as well. The plugin that merges features based on taxonomy does not (as far as I know) also merge tree tips. So once you merge, you lose your tree and can’t use phylogenetic metrics anymore. :cry:

Someone should open an issue about this!

Also, I would love to know how Phyloseq and the R package ape does this. Phylogeny != taxonomy, so getting a realistic tree from merged features is non-trivial.

Who’s the Q2 person I should ping about tree questions?


just an fyi, this is the response I got from iTOL regarding this issue,

'iTOL has basic tree editing functions, check the help for details. Click on any node, tree structure submenu (or something like that, cannot check the spelling now) ’

not overly helpful, ill keep looking into it, and see what I can do.


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