I need to export a newick tree displayed by genus level/any taxonomic level, so I could annotate and visualize the tree in other open sources.
The tree is displayed by OTUIDs, even after agglomeration (in R) still displayed by OTUID.
Is there any solution in qiime2?
The short answer is you currently can’t do that within Qiime2 itself. But see this post with an example of how to do this outside using an interactive tree building tool like iTOL.
That being said, if you have your tree, taxonomy and table you should already be able to do this within R if you are using something like phyloseq which accepts taxonomy files and can use those as tree tip names.
Thank you @Mehrbod_Estaki, it is okay but still simple, I mean I wish if I could collapse to a specific taxonomic level and add metadata as well!!
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