pplacer

pplacer is a tool for phylogenetic placement, a version of phylogenetic tree construction, and visualization.

Topic

Evolutionary biology;Population genetics;Phylogeny

Detail

  • Operation: Phylogenetic tree reconstruction; Visualization

  • Software interface: Command-line user interface

  • Language: C, Python

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.1.alpha19

  • Credit: The Miller Institute for Basic Research at the University of California, Berkeley, the University of Washington Friday Harbor Laboratories, Gordon and Betty Moore Foundation Marine Microbiology.

  • Input: -

  • Output: -

  • Contact: Frederick A Matsen ematsen@gmail.com, Frederick A Matsen matsen@fhcrc.org, Robin B Kodner rkodner@u.washington.edu, E Virginia Armbrust armbrust@u.washington.edu

  • Collection: -

  • Maturity: -

Publications

  • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
  • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010 Oct 30;11:538. doi: 10.1186/1471-2105-11-538. PMID: 21034504; PMCID: PMC3098090.
  • https://doi.org/10.1186/1471-2105-11-538
  • PMID: 21034504
  • PMC: PMC3098090

Download and documentation

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