why we dont see result of alpha diversity metrics (Shannon’s, Faith’s Phylogenetic Diversity,...) in this command for calculate core-metrics-phylogenetic just generates principle coordinates analysis (PCoA) plots for each of the beta diversity metrics.
You can use alpha-group-significance to create visualization based on those alpha diversity metrics. Also see this section for a great overview of what other analyses you can do that are outside of core-metrics.
thank you so much your response. I have question else. how can i build phylogenetic tree in qiime 2 ?
If you are new to this type of analyses I strongly recommend initially going over the qiime2 overview tutorial which explains the phylogenetic tree building process as well as following through an example data set like the moving pictures tutorial which shows exactly how this is done as well.
An off-topic reply has been split into a new topic: Finding the right greengenes files for training a classifier
Please keep replies on-topic in the future.
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