Converting file to .tre or .nexus?

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Hi everyone,

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 (GitHub - biocore/empress: A fast and scalable phylogenetic tree viewer for microbiome data analysis), 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!

Thanks,
Sam

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Hello Sam,

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. :evergreen_tree:

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! :palm_tree:

Let us know what you find,
Colin

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Thanks Colin! Didn't realize it would be such an easy fix :slightly_smiling_face:

I'm working on learning R now, so once I figure out how to import my data, I'll give the plot_tree() function a try.

Sam

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