I have a phylogeny file as a .qza, .qzv, and .nwk and need to convert it to a .nexml, .dendro, .tre, or .nexus. Any ideas on how to do this?
I built a phylogeny of some metagenomic 16S data using iqtree, which saved the file as a .qza. I have also used Empress (https://github.com/biocore/empress), which converted the tree to a .qzv. I also used qiime tools export, which converted the .qzv to a .nwk. I am trying to visualize this tree with Dendroscope, which only takes the above file formats.
I’m using Dendroscope because my tree is relatively big (~18000 taxa), and is not easily viewable with iTOL or other phylogeny viewing software. I heard that Dendroscope may be able to handle a tree of that size. If anyone has any other software that may work to view the tree, that would solve my problem as well!
I think you are in luck! When you open up the .qza, that tree file inside there is in the Newick tree format (so .tre == .nwk). It sounds like this is supported by Dendroscope.
I’ve used phyloseq to plot large trees before, but I’m not sure how familiar you are with R. If you have used R, then I think phyloseq and the plot_tree() function is a great place to start!