Phylogenetic Placement

We recommend our review article as an introduction to the topic of phylogenetic placement:

Metagenomic Analysis Using Phylogenetic Placement — A Review of the First Decade.
Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera.
Frontiers in Bioinformatics, 2022. https://doi.org/10.3389/fbinf.2022.871393

The most common programs for conducting this analysis are EPA-ng, RAxML-EPA and pplacer. They usually store the data in jplace files, which is what many gappa commands work with.

For a full stack example of using placement with EPA-ng, see here.