software
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<div>1) Extracts a subtree from the GTDB overall tree based on taxonomy. In this case, Omnitrophota and Ratteibacteria.</div><div>2) Build a fake pplacer refpkg based on the original info in the GTDB refpkg.</div><div>3) Run pplacer on the subtree using the model info for the larger tree</div><div>4) Regraft the subtree back into the main treee</div><div><br></div><div>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.<br></div>