| name | phylogenomics |
| description | 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.
|
| license | MIT |
| category | orchestration |
| tags | ["phylogeny","tree","IQ-TREE","PhyloPhlAn","evolution","GTDB","routing"] |
| stage | taxonomy |
Phylogenomics / evolutionary routing
Taxonomy labels, species ANI, and phylogenetic trees are different claims.
This hub routes evolutionary analyses after HQ genomes/MAGs exist.
Analytical thinking
| Need | Prefer | Notes |
|---|
| Bacterial/archaeal MAG taxonomy | gtdbtk (+ gtdb) | Placement into GTDB; pin release |
| Multi-genome / MAG phylogeny | phylophlan | Marker sets + tree; feed iqtree/fasttree |
| Structural core-gene phylogeny | unicore | Foldseek/ProstT5 cores (Steinegger) |
| Publication-grade ML tree | iqtree | ModelFinder, UFBoot; after MSA |
| Fast approximate tree (large MSA) | fasttree | Screen / draft; upgrade to IQ-TREE for final |
| Alignment-free PLM / hyperbolic phylo | lucaphylo | Divergent proteins; experimental vs classical MSA |
| Species / strain boundary | skani · fastani | Distance, not a tree |
| Gene tree vs species tree | State clearly | HGT / paralogs break naive concatenation |
Hard rules:
- Filter with
checkm2 / gunc before tree claims
- Pin alignment + model + bootstrap / UFBoot settings
- Do not treat ANI clusters as phylogenies
- AI/PLM trees (
lucaphylo) are complementary — do not replace GTDB-Tk Methods
without justification
- Research talks (evolutionary LMs, trajectory models) are frontier context only —
not production defaults here
RAxML-NG / ASTRAL remain valid for specialized species-tree workflows; prefer
documenting them explicitly if used instead of IQ-TREE2.
Decision tree
Evolutionary / tree need?
│
├─ Assign MAG to GTDB taxonomy → gtdbtk
├─ Build genome phylogeny from many MAGs → phylophlan
│ ├─ Draft / huge MSA → fasttree
│ └─ Final ML tree → iqtree
├─ Structural core genes / 3Di → unicore
├─ Species demarcation (ANI) → skani / fastani
├─ Highly divergent proteins, MSA fails → lucaphylo (± classical backup)
└─ Homology search only (not a tree) → homology-search
Related skills
gtdbtk · gtdb · phylophlan · unicore · iqtree · fasttree ·
lucaphylo · foldseek · foldmason · skani · fastani ·
homology-search · metagenomics-llm · mag-qc · tool-selection
