phylophlan

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
# follow upstream tutorials for database setup + config
# typical: genomes/ → phylophlan → MSA + tree (optionally refine with iqtree)
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