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Hi Lucas,
I just read your paper on Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples, which illustrated the benefits of incorporating phylogeny into the analysis of microbiome data. The paper is well-written and easy to digest.
Just out of curiosity, is there any chance that you would develop a QIIME2 plugin to implement the methods introduced in the paper? I believe that a QIIME2 plugin would make it easier to use the tool and expose it to more researchers working on the microbiome data, though it would certainly add extra workload to you and your coauthors.
In case you are interested, here the link to QIIME2 plugins which has many applications now.
Best,
Yanxian