| name | phylophlan |
| description | PhyloPhlAn 3 — precise phylogenetic analysis of microbial isolates and metagenome-assembled genomes via marker sets, alignment, and tree building. Use when: (1) Reconstructing phylogenies across many MAGs/genomes, (2) Contextualizing novel lineages beyond a single GTDB-Tk row, (3) Generating inputs for IQ-TREE/FastTree. Upstream: https://github.com/biobakery/phylophlan. Route via phylogenomics.
|
| license | MIT |
| category | analysis-tools |
| tags | ["PhyloPhlAn","phylogeny","MAG","markers","tree"] |
| upstream | https://github.com/biobakery/phylophlan |
| stage | taxonomy |
PhyloPhlAn
Upstream: biobakery/phylophlan ·
https://huttenhower.sph.harvard.edu/phylophlan
Citation
Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and
genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500
(2020). https://doi.org/10.1038/s41467-020-16366-7
Segata, N. et al. PhyloPhlAn is a new method for improved phylogenetic and
taxonomic placement of microbes. Nat. Commun. 4, 2304 (2013).
https://doi.org/10.1038/ncomms3304
See also docs/references.md.
Analytical thinking
PhyloPhlAn automates marker selection → alignment → tree for isolates and
MAGs. Use when GTDB-Tk classification is not enough (custom clades, publication
trees, multi-study genome sets). Tree quality still depends on genome QC and
chosen database/config.
| vs | Prefer PhyloPhlAn when |
|---|
gtdbtk | Need a reconstructed phylogeny, not only taxonomy labels |
Manual iqtree | Want an end-to-end MAG phylogenomics workflow |
lucaphylo | Standard marker MSA phylogeny is appropriate |
How to run
conda install -c bioconda phylophlan
phylophlan -i genomes/ -o temp/phylophlan/ -d phylophlan \
--diversity medium -f YOUR.cfg --nproc 16
Exact flags depend on installed PhyloPhlAn configs — pin version and config
name in Methods.
Decision tree
Many MAGs need a phylogeny?
├─ Taxonomy labels only → gtdbtk
├─ Marker-based genome tree workflow → phylophlan
│ └─ Optional final ML → iqtree
├─ Single MSA already in hand → iqtree / fasttree
└─ Extreme divergence / no MSA → lucaphylo
Related skills
phylogenomics · iqtree · fasttree · gtdbtk · gtdb · mag-qc ·
checkm2 · tool-selection
