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Subtree-grafting python script

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posted on 2022-08-14, 04:15 authored by Cale SeymourCale Seymour, Marike PalmerMarike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik SchulzFrederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian-Yu Jiao, Zheng-Shuang Hua, Lan Liu, Zheng-Han Lian, Wen-Jun Li, Maria Chuvochina, Brianna Finley, Benjamin J. Koch, Duane P. Moser, Bruce A. Hungate, Brian P. Hedlund
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 tree
4) 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.