recipe phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes



MIT / MIT License



PhyloPhlAn 3.0 is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn 3.0 is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs). PhyloPhlAn 3.0 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.

package phylophlan

(downloads) docker_phylophlan



depends biopython:


depends blast:


depends dendropy:


depends diamond:


depends fasttree:


depends iqtree:


depends mafft:


depends mash:

depends matplotlib-base:


depends muscle:


depends numpy:


depends pandas:


depends python:


depends raxml:


depends requests:

depends seaborn:


depends trimal:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install phylophlan

and update with::

   mamba update phylophlan

To create a new environment, run:

mamba create --name myenvname phylophlan

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `phylophlan/tags`_ for valid values for ``<tag>``)

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