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About the PhyloPhlAn category

Name: PhyloPhlAn
User manual || Tutorial

Description: PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information.
The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also
implements taxonomic curation, estimation, and insertion operations.

The main features of PhyloPhlAn are:

  • completely automatic, as the user needs only to provide the (unannotated) protein sequences of the input genomes (as multifasta files of peptides - not nucleotides)
  • very high topological accuracy and resolution because of the use of up to 400 previously identified most conserved proteins
  • the possibility of integrating new genomes in the already reconstructed most comprehensive tree of life (3,171 microbial genomes)
  • taxonomy estimation for the newly inserted genomes
  • taxonomic curation for the produced phylogenetic trees


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

Nature Communications, vol. 11, p. 2500, May 2020 10.1038/s41467-020-16366-7