Scalable and Accurate Phylogenetic Placement Using pplacer-XR

Phylogenetic placement, the problem of placing a sequence into a precomputed phylogenetic “backbone” tree, is useful for constructing large trees, performing taxon identification of newly obtained sequences, and other applications. The most accurate current method, pplacer, performs the placement using maximum likelihood but fails frequently on backbone trees with 5000 sequences. We show a simple technique, pplacer-XR (pplacer-eXtra Range), that extends pplacer to large datasets. We show, using challenging large datasets, that pplacer-XR provides the accuracy of pplacer and the scalability to ultra-large datasets of a leading fast phylogenetic placmement method, APPLES. pplacer-XR is available in open source form on github.