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


3.0-5, 3.0-4, 3.0-2, 3.0-1, 3.0-0

Required By


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install phylophlan

and update with:

conda update phylophlan

or use the docker container:

docker pull<tag>

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