Beta diversity rarefaction - Newick file not viewable

Hi, this might be a silly question, but I’ve run the following command:

qiime diversity beta-rarefaction --i-table Eunonly-filtered-table.qza --p-metric braycurtis --p-clustering-method nj --m-metadata-file eunsamples-to-keep.csv --p-sampling-depth 800 --p-iterations 20 --o-visualization betararefaction-eun-only-800.qzv

Which worked well and I was easily able to view the emperor plot, however, when I download the Newick tree file it downloads as an .html file and can’t be used to make any viewable tree. Am I doing something wrong in the command that this isn’t viewable? Or am I doing something wrong when I download the file and try to use the online viewer and it just tells me its a .html file and there is nothing else? Seems like it must be something simple I’m missing.


Hello Alicia,

Would you be willing to post your output .qzv file so we can take a look?


Hi @reige012, have you tried “right-clicking” on the download button and picking “save file as” (or something similar, depending on your browser)?

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