New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings.

Software repository and supporting material

The software repository of PhyloPhlAn is at:
The supporting user group is at:!forum/phylophlan-users
An introductory tutotial is available at:
A Galaxy interface is at:
For comments and question please refer to the user group linked above or contact us


If you find the tool useful in your research, please cite our paper:

Nicola Segata Daniela Börnigen Xochitl C. Morgan Curtis Huttenhower

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

Nature Communications, vol. 4, p. 2304, Jul. 2013 10.1038/ncomms3304