Scalable and Accurate Phylogenetic Placement Using pplacer-XR

Eleanor Wedell, Yirong Cai, Tandy Warnow

Research output: Chapter in Book/Report/Conference proceedingConference contribution


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.

Original languageEnglish (US)
Title of host publicationAlgorithms for Computational Biology - 8th International Conference, AlCoB 2021, Proceedings
EditorsCarlos Martín-Vide, Miguel A. Vega-Rodríguez, Travis Wheeler
Number of pages12
ISBN (Print)9783030744311
StatePublished - 2021
Externally publishedYes
Event8th International Conference on Algorithms for Computational Biology, AlCoB 2021 - Missoula, United States
Duration: Jun 7 2021Jun 11 2021

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12715 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference8th International Conference on Algorithms for Computational Biology, AlCoB 2021
Country/TerritoryUnited States


  • Likelihood-based methods
  • Phylogenetic placement
  • Phylogenetics

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


Dive into the research topics of 'Scalable and Accurate Phylogenetic Placement Using pplacer-XR'. Together they form a unique fingerprint.

Cite this