PhyloPhlAn

High-resolution Microbial Phylogenetics

What is PhyloPhlAn?

PhyloPhlAn is a tool for high-resolution microbial phylogeny reconstruction, genome characterization, and taxonomic assignment of microbial genomes. It uses a large database of universal single-copy marker proteins to build comprehensive and accurate phylogenetic trees from whole genomes or metagenome-assembled genomes (MAGs).

PhyloPhlAn answers the question: “Where does this genome fit on the tree of life?”

Current version: PhyloPhlAn 3

📄 GitHub
📖 Documentation
🗞️ Paper: Asnicar et al. 2020, Nature Communications

When to Use PhyloPhlAn

Use PhyloPhlAn when you want to:

Place new genomes or MAGs on a reference phylogenetic tree
Characterize the taxonomy of novel organisms
Build high-quality, large-scale phylogenetic trees
Assign taxonomy to unannotated genomes

Installation

Via conda (recommended)

conda create -n phylophlan -c bioconda -c conda-forge phylophlan
conda activate phylophlan

Via pip

pip install phylophlan

External dependencies

PhyloPhlAn requires: - mash — for initial genome sketching and clustering - muscle or mafft — for multiple sequence alignment - trimal — for alignment trimming - raxml or iqtree — for phylogenetic tree inference

Install all at once via conda:

conda install -c bioconda mash muscle mafft trimal raxml iqtree

Basic Usage

Database setup

# List available databases
phylophlan_databases --help

# Download a database (e.g., for genome phylogeny)
phylophlan_setup_database \
  -d phylophlan \
  --database_folder databases/

Phylogenetic tree construction

phylophlan \
  -i genome_folder/ \
  -d phylophlan \
  --databases_folder databases/ \
  -o output_tree/ \
  --diversity medium \
  --nproc 8 \
  -f supermatrix_aa.cfg

Metagenomic strain tracking

phylophlan_metagenomic \
  -i mag_folder/ \
  -d SGB.Jan19 \
  --databases_folder databases/ \
  -o output_sgbs/ \
  --nproc 8

Key Modes

Mode	Command	Use case
Genome phylogeny	`phylophlan`	Build trees from genomes
MAG classification	`phylophlan_metagenomic`	Assign MAGs to SGBs
Database creation	`phylophlan_setup_database`	Build custom databases

Output Files

File	Contents
`*.tre`	Newick-format phylogenetic tree
`*.xml`	PhyloXML-format tree
`*_refined.tre`	Tree after outlier removal

Tips & Gotchas

Tip

Choose the right diversity setting — Use --diversity low for closely related strains, medium for species-level analyses, and high for genus/family-level trees.

Warning

Input genome quality matters — Highly fragmented or low-quality genomes (e.g., MAGs with <50% completeness) may produce poorly placed branches. Filter by completeness using CheckM first.

Tip

PhyloPhlAn integrates with MetaPhlAn — MetaPhlAn’s SGB (Species-level Genome Bins) taxonomy is based on PhyloPhlAn trees.

--- title: "PhyloPhlAn" subtitle: "High-resolution Microbial Phylogenetics" --- ## What is PhyloPhlAn? **PhyloPhlAn** is a tool for high-resolution microbial phylogeny reconstruction, genome characterization, and taxonomic assignment of microbial genomes. It uses a large database of universal single-copy marker proteins to build comprehensive and accurate phylogenetic trees from whole genomes or metagenome-assembled genomes (MAGs). PhyloPhlAn answers the question: **"Where does this genome fit on the tree of life?"** Current version: **PhyloPhlAn 3** - 📄 [GitHub](https://github.com/biobakery/phylophlan) - 📖 [Documentation](https://github.com/biobakery/phylophlan/wiki) - 🗞️ [Paper: Asnicar et al. 2020, *Nature Communications*](https://www.nature.com/articles/s41467-020-16366-7) --- ## When to Use PhyloPhlAn Use PhyloPhlAn when you want to: - Place new genomes or MAGs on a reference phylogenetic tree - Characterize the taxonomy of novel organisms - Build high-quality, large-scale phylogenetic trees - Assign taxonomy to unannotated genomes --- ## Installation ### Via conda (recommended) ```bash conda create -n phylophlan -c bioconda -c conda-forge phylophlan conda activate phylophlan ``` ### Via pip ```bash pip install phylophlan ``` ### External dependencies PhyloPhlAn requires: - `mash` — for initial genome sketching and clustering - `muscle` or `mafft` — for multiple sequence alignment - `trimal` — for alignment trimming - `raxml` or `iqtree` — for phylogenetic tree inference Install all at once via conda: ```bash conda install -c bioconda mash muscle mafft trimal raxml iqtree ``` --- ## Basic Usage ### Database setup ```bash # List available databases phylophlan_databases --help # Download a database (e.g., for genome phylogeny) phylophlan_setup_database \ -d phylophlan \ --database_folder databases/ ``` ### Phylogenetic tree construction ```bash phylophlan \ -i genome_folder/ \ -d phylophlan \ --databases_folder databases/ \ -o output_tree/ \ --diversity medium \ --nproc 8 \ -f supermatrix_aa.cfg ``` ### Metagenomic strain tracking ```bash phylophlan_metagenomic \ -i mag_folder/ \ -d SGB.Jan19 \ --databases_folder databases/ \ -o output_sgbs/ \ --nproc 8 ``` --- ## Key Modes | Mode | Command | Use case | |------|---------|----------| | Genome phylogeny | `phylophlan` | Build trees from genomes | | MAG classification | `phylophlan_metagenomic` | Assign MAGs to SGBs | | Database creation | `phylophlan_setup_database` | Build custom databases | --- ## Output Files | File | Contents | |------|----------| | `*.tre` | Newick-format phylogenetic tree | | `*.xml` | PhyloXML-format tree | | `*_refined.tre` | Tree after outlier removal | --- ## Tips & Gotchas ::: {.callout-tip} **Choose the right diversity setting** — Use `--diversity low` for closely related strains, `medium` for species-level analyses, and `high` for genus/family-level trees. ::: ::: {.callout-warning} **Input genome quality matters** — Highly fragmented or low-quality genomes (e.g., MAGs with <50% completeness) may produce poorly placed branches. Filter by completeness using CheckM first. ::: ::: {.callout-tip} **PhyloPhlAn integrates with MetaPhlAn** — MetaPhlAn's SGB (Species-level Genome Bins) taxonomy is based on PhyloPhlAn trees. ::: --- ## Further Reading - [PhyloPhlAn3 tutorial](https://github.com/biobakery/biobakery/wiki/phylophlan) - [Asnicar et al. 2020, *Nature Communications*](https://www.nature.com/articles/s41467-020-16366-7)