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.