Export phyloseq to qiime2

I have a phyloseq object, and I am interested in exporting phyloseq to QIIME2. I have a biom table and tree file which I obtained using

tree.seq = phy_tree(physeq)
ape::write.tree(tree.seq, “sequencing.phylogenetic_tree.tree”)

and converted biom table to qza file using -

qiime tools import --input-path otu_table.biom --output-pathotu_table.biom.qza --type FeatureTable[Frequency]

is there a way where I can export tree file to QIIME2 as well.


Hi @shashankgpt! Once you’ve saved a Newick tree file using phyloseq, you can import the Newick file following this section of the importing tutorial. The example in the tutorial assumes you have an unrooted phylogenetic tree. If your tree is already rooted, you can import the Newick file using --type Phylogeny[Rooted].

Thanks. That works.

Now I have “otu.table.biom.qza” and “rooted.tree.qza” obtained from phyloseq and converted to .qza format, I am still confused about how can I generate it to "taxonomy.qza"
I am interested in making plots using QIIME2.

I was looking at the scripts on the tutorial, but I don’t know from where I can get the other information -

qiime feature-classifier classify-sklearn
–i-classifier gg-13-8-99-515-806-nb-classifier.qza
–i-reads rep-seqs.qza
–o-classification taxonomy.qza

qiime metadata tabulate
–m-input-file taxonomy.qza
–o-visualization taxonomy.qzv

Glad the export/import steps worked for you! You’ll need to import representative sequences (see this section of the importing tutorial) in order to perform taxonomic classification. Each representative sequence corresponds to a “feature” in the feature table – in this case it looks like your “features” are OTUs, so you’ll have a single representative sequence per OTU.

If you haven’t already, I recommend working through the Getting Started guide and the Moving Pictures tutorial, which explain these concepts in more detail, along with example data.

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