biobakery/phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

PhyloPhlAn

PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs). PhyloPhlAn can reconstruct strain-level phylogenies using clade-specific maximally informative phylogenetic markers, and can also scale to very-large phylogenies comprising >17,000 microbial species.

Installation

Bioconda

You can install PhyloPhlAn using conda as follows:

conda install -c bioconda phylophlan

Repository

You can clone the PhyloPhlAn repository from GitHub:

git clone https://github.com/biobakery/phylophlan
cd phylophlan
python setup.py install

Then remember to check that the Dependencies and Tools are in stalled and available in your system.

Tutorials

• PhyloPhlAn User manual
• PhyloPhlAn Tutorials
• PhyloPhlAn Example 1: Phylogenetic characterization of isolate genomes of a given species (S. aureus)
• PhyloPhlAn Example 2: Prokaryotes Tree of life reconstruction
• PhyloPhlAn Example 3: Metagenomic analysis of the Ethiopian cohort
• PhyloPhlAn Example 4: High-resolution phylogeny of genomes and MAGs of a known species (E. coli)
• PhyloPhlAn Example 5: Phylogenetically characterization of an unknown SGB from the Proteobacteria phylum

Support

We provide support through the bioBakery help forum and through the issues tracking system of the PhyloPhlAn repository.

Citation

If you used PhyloPhlAn please cite the following paper:

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, and Nicola Segata
Nat Commun 11, 2500 (2020)
DOI: https://doi.org/10.1038/s41467-020-16366-7