I am looking for suggestions regarding when you should make a phylogenetic tree. I used deblur to process my dataset. Should the tree be made with the rep-seqs from the deblur output? After deblur, I removed mitochondria and chloroplast sequences from my dataset. I also filtered by taxon frequency, reducing my total number of taxa from 2,016 (deblur output) to 898. Should the tree then be made only with the 898 taxa? Does having more sequences in the alignment improve the quality? Will the weighted unifrac distances be compromised if taxa present in the tree are not also present in the biom table?
I appreciate any recommendations.