I have some doubts.
I used dada2 to denoise my data and followed the “moving pictures” tutorial to generate the outputs. I already generated the .qza for the rooted and unrooted trees and the core-metrics directory with the .qza and .qzv outputs.
I would like to plot a phylogenetic tree and calculate Faith’s phylogenetic diversity per sample in R, but I’m confused about which files I should import to R and which R packages I could use to calculate the PD and plot the tree.
Hope someone can help me.
Thanks in advance!