1. Deviations between de novo or insertion trees and gold standard trees.
Deviations between de novo or insertion trees and gold standard trees. For 100 iterations, we randomly chose 10, nt V4 fragments to split the Greengenes tree into training and testing trees. Phylogenies for the 10,000 fragments were constructed via QIIME2’s de novo recommendations and SEPP. For both metrics, the insertion trees were significantly (two-sided Mann-Whitney tests; P < 10−32) closer to the gold standard than the de novo trees. The tip-to-tip distance summarizes the similarity of two trees as the Pearson correlation coefficient of two sets of path lengths, where pairs with tips not present in both trees are omitted. Those two sets are independently enumerated as pairwise tip-to-tip path lengths for each tree.
Stefan Janssen et al. mSystems 2018; doi: /mSystems