Route phylogenetic and evolutionary analyses for shotgun metagenomics and MAGs: GTDB-Tk placement, genome/marker trees (PhyloPhlAn, IQ-TREE, FastTree), alignment-free PLM phylogeny (LucaPhylo), and ANI species boundaries (skani/FastANI). Use when building or interpreting trees, placing genomes, or choosing classical vs AI phylogeny — not for read profilers alone.
