The Huttenhower Lab > phylophlan
PhyloPhlAn 3.0

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.

For more information on the technical aspects of:

User manual || Tutorial || Forum

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, Nicola Segata

In press

  1. Completely automatic, as the user needs only to provide the (unannotated) protein sequences of the input genomes (as multifasta files of peptides – not nucleotides)
  2. Very high topological accuracy and resolution because of the use of up to 400 previously identified most conserved proteins
  3. The possibility of integrating new genomes in the already reconstructed most comprehensive tree of life (3,171 microbial genomes)
  4. Taxonomy estimation for the newly inserted genomes
  5. Taxonomic curation for the produced phylogenetic trees


PhyloPhlAn 3.0 is released in Bioconda and can be installed using the following command:

conda install -c bioconda phylophlan