I am wanting to create an UPGMA tree using a UniFrac distance matrix. I have done this in QIIME1, and am wondering if it will be an option in QIIME2? Additionally, I’d like to make an OTU network tree to do Cytoscape anlaysis on, which is also available in QIIME1. Will these tools be available in QIIME 2 eventually (or are they already and I’m just missing it? I know I can probably export my data and analyze in R, but I’m not R saavy…Thank you!
Hi @linneakh!
Unfortunately, UPGMA is not yet supported in QIIME 2; we will be adding it within the next release or two (2017.8 or 2017.9). I created an issue to track progress and we'll follow up here when UPGMA support is in a release.
Additionally, we are working on a basic qiime diversity beta-rarefaction visualizer, which will be included in the upcoming 2017.8 release. This visualizer is analogous to QIIME 1's jackknifed_beta_diversity.py script. The initial version won't support jackknifed/bootstrapped UPGMA trees nor Emperor plots with confidence ellipsoids, but the next iteration on beta-rarefaction will include these components. These features will likely be added in the 2017.9 release.
We also don't have that support in QIIME 2 yet. QIIME 1's make_otu_network.py support is on our radar but not as high of a priority as other features (e.g. UPGMA). We will have network analysis support by the end of 2017 in an effort to match QIIME 1 feature parity.
You could trying exporting your data using qiime tools export and use the exported data with the corresponding QIIME 1 scripts. For example, you could export your UniFrac distance matrix .qza file and use it with QIIME 1's upgma_cluster.py script.
Hope this helps!
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QIIME 2 2017.12 was just released and it adds sample-clustering and jackknifed PCoA to diversity beta-rarefaction. You can choose "upgma" as your clustering method.
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