Subtree-grafting python script

  • Cale O. Seymour (Creator)
  • Marike Palmer (Creator)
  • Eric D. Becraft (Creator)
  • Ramunas Stepanauskas (Creator)
  • Ariel D. Friel (Creator)
  • Frederik Schulz (Creator)
  • Tanja Woyke (Creator)
  • Emiley A. Eloe-Fadrosh (Creator)
  • Dengxun Lai (Creator)
  • Jian Yu Jiao (Creator)
  • Zheng Shuang Hua (Creator)
  • Zheng Han Lian (Creator)
  • Maria Chuvochina (Creator)
  • Brianna K. Finley (Creator)
  • Benjamin J. Koch (Creator)
  • Bruce A. Hungate (Creator)
  • Brian P. Hedlund (Creator)



1) Extracts a subtree from the GTDB overall tree based on taxonomy. In this case, Omnitrophota and Ratteibacteria.2) Build a fake pplacer refpkg based on the original info in the GTDB refpkg.3) Run pplacer on the subtree using the model info for the larger tree4) Regraft the subtree back into the main treee This procedure bypasses the large memory requirement for GTDB, in cases where you can roughly identify the higher-order taxonomy for your genomes. Since there are many genomes in GTDB that represent Omnitrophota, this is possible for this lineage. Otherwise, use with caution.
Date made available2022

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