From qiime2 to R : how to transform a .qza to .tre


I would like to export my rooted-tree.qza in R and work with phyloseq. For this I would need .tre format for the three.
How can you export your .qza in .tre?

Thank you very much,


Hi @leila,

You can use the export command to get your tree file. The file will be in newick format (.nwk) though and not .tree, but I do believe this should still be fine with phyloseq.


Thanks @Mehrbod_Estaki!

I’ve seen the file extensions .nwk, .tre, and .tree all used interchangeably with Newick files (I don’t think there’s much of a standard there). QIIME 2 generally doesn’t care about file extensions, though I’m unsure about phyloseq. @leila, if phyloseq isn’t able to import the file with .nwk extension, you could try renaming the file to use .tre extension.

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