SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees.

Phylogenetic placement, the problem of placing a "query" 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 methods, such as pplacer and EPA-ng, are based on maximum likelihood and require that the query sequence be provided within a multiple sequence alignment that includes the leaf sequences in the backbone tree. This approach enables high accuracy but also makes these likelihood-based methods computationally intensive on large backbone trees, and can even lead to them failing when the backbone trees are very large (e.