Abstract
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.
Y. Cai and E. Wedell—Contributed equally to this work.
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Acknowledgments
The research presented here is the result of a course project by EW and YC for the Spring 2020 course CS 581: Algorithmic Genomic Biology, at the University of Illinois, taught by TW. This work was supported in part by the National Science Foundation grant ABI-1458652 to TW.
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Appendix
Appendix
Commands to create backbone trees: All placement methods use the same backbone tree topologies, but have different branch lengths (following the protocol as provided in [2]). We downloaded the backbone trees with their optimized branch lengths for each phylogenetic placement method from the APPLES repository.
On replicates 1 and 2 of the 100,000-leaf backbone condition and replicate 0 of the 200,000-leaf replicate backbone condition, each containing more than two identical sequences, the backbone trees had polytomies. We randomly resolved these in order to run RAxML.
Random tree refinement: raxmlHPC-PTHREADS -f e -t res_true.fasttree -m GTRGAMMA -s aln_dna.phy -n REF -p 1984 -T 16
APPLES command: run_apples.py -t backbone.tree -s ref.fa -q query.fa -T 16 -o apples.jplace
EPA-ng command: epa-ng –ref-msa ref.fa –tree backbone.tree –query query.fa –outdir $query –model RAxML_info.REF8 –redo -T 16
pplacer-XR commands: python3 pplacer-XR.py GTR RAxML_info.REF backbone.tree output_dir aln.fa query.txt 2000
Github site: https://github.com/chry04/pplacer_plusplus
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Wedell, E., Cai, Y., Warnow, T. (2021). Scalable and Accurate Phylogenetic Placement Using pplacer-XR. In: Martín-Vide, C., Vega-Rodríguez, M.A., Wheeler, T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science(), vol 12715. Springer, Cham. https://doi.org/10.1007/978-3-030-74432-8_7
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